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HEADER OXYGEN STORAGE/TRANSPORT 15-MAY-02 1IWH TITLE CRYSTAL STRUCTURE OF HORSE CARBONMONOXYHEMOGLOBIN- TITLE 2 BEZAFIBRATE COMPLEX AT 1.55A RESOLUTION: A NOVEL TITLE 3 ALLOSTERIC BINDING SITE IN R-STATE HEMOGLOBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: HEMOGLOBIN BETA CHAIN; COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 TISSUE: BLOOD; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 7 ORGANISM_COMMON: HORSE; SOURCE 8 TISSUE: BLOOD KEYWDS HORSE, HEMOGLOBIN, LIGAND-BEZAFIBRATE, KEYWDS 2 CARBONMONOXYHEMOGLOBIN EXPDTA X-RAY DIFFRACTION AUTHOR N.SHIBAYAMA,S.MIURA,J.R.H.TAME,T.YONETANI,S.-Y.PARK REVDAT 2 06-MAY-03 1IWH 1 JRNL REVDAT 1 02-OCT-02 1IWH 0 JRNL AUTH N.SHIBAYAMA,S.MIURA,J.R.H.TAME,T.YONETANI,S.-Y.PARK JRNL TITL CRYSTAL STRUCTURE OF HORSE JRNL TITL 2 CARBONMONOXYHEMOGLOBIN-BEZAFIBRATE COMPLEX AT JRNL TITL 3 1.55A RESOLUTION. A NOVEL ALLOSTERIC BINDING SITE JRNL TITL 4 IN R-STATE HEMOGLOBIN JRNL REF J.BIOL.CHEM. V. 277 38791 2002 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.174 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.175 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2038 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38739 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.151 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.151 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1438 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 27422 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2203 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 115 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2638.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10557 REMARK 3 NUMBER OF RESTRAINTS : 9428 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.082 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.022 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.036 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.071 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IWH COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-29) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ . REMARK 100 THE RCSB ID CODE IS RCSB005341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-2002 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR165MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1000, PH 6.8, SMALL TUBES, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 -X,Y,1/2-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 1/2+X,1/2+Y,Z REMARK 290 6555 1/2-X,1/2-Y,1/2+Z REMARK 290 7555 1/2-X,1/2+Y,1/2-Z REMARK 290 8555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.37250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.37250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.19800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.74800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.19800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.74800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.37250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.19800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 53.74800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.37250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.19800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 53.74800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 214.99200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 173.49000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 1001 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 82 CG ASN A 82 ND2 -0.077 REMARK 500 ASP A 85 CG ASP A 85 OD2 0.087 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 105 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU B 288 CA - CB - CG ANGL. DEV. =-13.0 DEGREES REMARK 500 LEU B 288 CB - CG - CD2 ANGL. DEV. = 12.0 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 1210 DISTANCE = 8.13 ANGSTROMS REMARK 525 HOH 1228 DISTANCE = 10.63 ANGSTROMS REMARK 525 HOH 1253 DISTANCE = 12.34 ANGSTROMS DBREF 1IWH A 1 141 UNP P01958 HBA_HORSE 1 141 DBREF 1IWH B 201 346 UNP P02062 HBB_HORSE 1 146 SEQRES 1 A 141 VAL LEU SER ALA ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 A 141 TRP SER LYS VAL GLY GLY HIS ALA GLY GLU TYR GLY ALA SEQRES 3 A 141 GLU ALA LEU GLU ARG MET PHE LEU GLY PHE PRO THR THR SEQRES 4 A 141 LYS THR TYR PHE PRO HIS PHE ASP LEU SER HIS GLY SER SEQRES 5 A 141 ALA GLN VAL LYS ALA HIS GLY LYS LYS VAL GLY ASP ALA SEQRES 6 A 141 LEU THR LEU ALA VAL GLY HIS LEU ASP ASP LEU PRO GLY SEQRES 7 A 141 ALA LEU SER ASN LEU SER ASP LEU HIS ALA HIS LYS LEU SEQRES 8 A 141 ARG VAL ASP PRO VAL ASN PHE LYS LEU LEU SER HIS CYS SEQRES 9 A 141 LEU LEU SER THR LEU ALA VAL HIS LEU PRO ASN ASP PHE SEQRES 10 A 141 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU SER SEQRES 11 A 141 SER VAL SER THR VAL LEU THR SER LYS TYR ARG SEQRES 1 B 146 VAL GLN LEU SER GLY GLU GLU LYS ALA ALA VAL LEU ALA SEQRES 2 B 146 LEU TRP ASP LYS VAL ASN GLU GLU GLU VAL GLY GLY GLU SEQRES 3 B 146 ALA LEU GLY ARG LEU LEU VAL VAL TYR PRO TRP THR GLN SEQRES 4 B 146 ARG PHE PHE ASP SER PHE GLY ASP LEU SER ASN PRO GLY SEQRES 5 B 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU HIS SER PHE GLY GLU GLY VAL HIS HIS LEU SEQRES 7 B 146 ASP ASN LEU LYS GLY THR PHE ALA ALA LEU SER GLU LEU SEQRES 8 B 146 HIS CYS ASP LYS LEU HIS VAL ASP PRO GLU ASN PHE ARG SEQRES 9 B 146 LEU LEU GLY ASN VAL LEU VAL VAL VAL LEU ALA ARG HIS SEQRES 10 B 146 PHE GLY LYS ASP PHE THR PRO GLU LEU GLN ALA SER TYR SEQRES 11 B 146 GLN LYS VAL VAL ALA GLY VAL ALA ASN ALA LEU ALA HIS SEQRES 12 B 146 LYS TYR HIS HET HEM A 142 43 HET CMO A 143 2 HET HEM B 347 43 HET CMO B 348 2 HET PEM 501 25 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETNAM PEM 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2- HETNAM 2 PEM METHYLPROPIONIC ACID HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CMO 2(C O) FORMUL 7 PEM C19 H20 CL N O4 FORMUL 8 HOH *295(H2 O) HELIX 1 1 SER A 3 VAL A 17 1 15 HELIX 2 2 HIS A 20 PHE A 36 1 17 HELIX 3 3 PRO A 37 PHE A 43 5 7 HELIX 4 4 SER A 52 GLY A 71 1 20 HELIX 5 5 ASP A 75 LEU A 80 1 6 HELIX 6 6 LEU A 80 LYS A 90 1 11 HELIX 7 7 ASP A 94 LEU A 113 1 20 HELIX 8 8 THR A 118 THR A 137 1 20 HELIX 9 9 SER B 204 ASP B 216 1 13 HELIX 10 10 ASN B 219 TYR B 235 1 17 HELIX 11 11 PRO B 236 GLY B 246 5 11 HELIX 12 12 ASN B 250 ASN B 257 1 8 HELIX 13 13 ASN B 257 HIS B 276 1 20 HELIX 14 14 ASN B 280 PHE B 285 1 6 HELIX 15 15 PHE B 285 ASP B 294 1 10 HELIX 16 16 PRO B 300 GLY B 319 1 20 HELIX 17 17 LYS B 320 PHE B 322 5 3 HELIX 18 18 THR B 323 ALA B 342 1 20 HELIX 19 19 HIS B 343 HIS B 346 5 4 LINK FE HEM A 142 NE2 HIS A 87 LINK FE HEM A 142 C CMO A 143 LINK FE HEM B 347 NE2 HIS B 292 LINK FE HEM B 347 C CMO B 348 LINK NC HEM B 347 C CMO B 348 CRYST1 62.396 107.496 86.745 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016027 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011528 0.00000