[Scop | Full Entry | Seq (local cached copy) | More Options ]
HEADER OXYGEN STORAGE/TRANSPORT 27-SEP-01 1IRD TITLE CRYSTAL STRUCTURE OF HUMAN CARBONMONOXY-HAEMOGLOBIN AT 1.25 TITLE 2 A RESOLUTION 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: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN KEYWDS ATOMIC RESOLUTION, STRUCTURE, CARBONMONOXY, HAEMOGLOBIN EXPDTA X-RAY DIFFRACTION AUTHOR S.-Y.PARK,J.R.H.TAME REVDAT 2 14-JAN-03 1IRD 1 REMARK REVDAT 1 17-OCT-01 1IRD 0 JRNL AUTH S.-Y.PARK,J.R.H.TAME JRNL TITL CARBONMONOXY-HAEMOGLOBIN AT 1.25 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 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) : 0.163 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.163 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3837 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 72937 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.159 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.159 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)) : 3362 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 64213 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2192 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 325 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2606.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 23458 REMARK 3 NUMBER OF RESTRAINTS : 28286 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.024 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.057 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.064 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.072 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IRD 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 RCSB005209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.70 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) : 0.7 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : SI(III) MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.53300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1HCO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM PHOSPHATE, PH 6.7, SMALL REMARK 280 TUBES, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 1/2-Y,1/2+X,1/4+Z REMARK 290 4555 1/2+Y,1/2-X,3/4+Z REMARK 290 5555 1/2-X,1/2+Y,1/4-Z REMARK 290 6555 1/2+X,1/2-Y,3/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,1/2-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 95.39000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.63500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.69500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.63500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.63500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.08500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.63500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.69500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.63500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 143.08500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 95.39000 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 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 2188 LIES ON A SPECIAL POSITION. REMARK 375 HOH 2283 LIES ON A SPECIAL POSITION. 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 HIS B 202 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 HIS B 202 CA - C - N ANGL. DEV. = 14.7 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 2124 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH 2236 DISTANCE = 5.33 ANGSTROMS DBREF 1IRD A 1 141 UNP P69905 HBA_HUMAN 1 141 DBREF 1IRD B 201 346 UNP P68871 HBB_HUMAN 1 146 SEQRES 1 A 141 VAL LEU SER PRO ALA ASP LYS THR ASN VAL LYS ALA ALA SEQRES 2 A 141 TRP GLY LYS VAL GLY ALA HIS ALA GLY GLU TYR GLY ALA SEQRES 3 A 141 GLU ALA LEU GLU ARG MET PHE LEU SER 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 GLY HIS GLY LYS LYS VAL ALA ASP ALA SEQRES 6 A 141 LEU THR ASN ALA VAL ALA HIS VAL ASP ASP MET PRO ASN SEQRES 7 A 141 ALA LEU SER ALA 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 VAL THR LEU ALA ALA HIS LEU PRO ALA GLU PHE SEQRES 10 A 141 THR PRO ALA VAL HIS ALA SER LEU ASP LYS PHE LEU ALA SEQRES 11 A 141 SER VAL SER THR VAL LEU THR SER LYS TYR ARG SEQRES 1 B 146 VAL HIS LEU THR PRO GLU GLU LYS SER ALA VAL THR ALA SEQRES 2 B 146 LEU TRP GLY LYS VAL ASN VAL ASP 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 GLU SER PHE GLY ASP LEU SER THR PRO ASP SEQRES 5 B 146 ALA VAL MET GLY ASN PRO LYS VAL LYS ALA HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU GLY ALA PHE SER ASP GLY LEU ALA HIS LEU SEQRES 7 B 146 ASP ASN LEU LYS GLY THR PHE ALA THR 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 CYS VAL LEU ALA HIS HIS SEQRES 10 B 146 PHE GLY LYS GLU PHE THR PRO PRO VAL GLN ALA ALA 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 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CMO CARBON MONOXIDE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CMO 2(C O) FORMUL 7 HOH *325(H2 O) HELIX 1 1 SER A 3 LYS A 16 1 14 HELIX 2 2 VAL A 17 ALA A 19 5 3 HELIX 3 3 HIS A 20 PHE A 36 1 17 HELIX 4 4 PRO A 37 PHE A 43 5 7 HELIX 5 5 SER A 52 HIS A 72 1 21 HELIX 6 6 ASP A 75 LEU A 80 1 6 HELIX 7 7 LEU A 80 LYS A 90 1 11 HELIX 8 8 PRO A 95 LEU A 113 1 19 HELIX 9 9 THR A 118 THR A 137 1 20 HELIX 10 10 THR B 204 GLY B 216 1 13 HELIX 11 11 GLU B 222 TYR B 235 1 14 HELIX 12 12 PRO B 236 GLY B 246 5 11 HELIX 13 13 THR B 250 ASN B 257 1 8 HELIX 14 14 ASN B 257 HIS B 277 1 21 HELIX 15 15 ASN B 280 ASP B 294 1 15 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 CRYST1 53.270 53.270 190.780 90.00 90.00 90.00 P 41 21 2 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 0.018772 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005242 0.00000