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HEADER OXYGEN TRANSPORT 25-SEP-96 1IBE TITLE DEOXY-HAEMOGLOBIN TRAPPED IN THE HIGH-AFFINITY (R) STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN (DEOXY); COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: HEMOGLOBIN (DEOXY); COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 6 ORGANISM_COMMON: HORSE KEYWDS HEME, OXYGEN TRANSPORT, RESPIRATORY PROTEIN, ERYTHROCYTE EXPDTA X-RAY DIFFRACTION AUTHOR J.WILSON,K.PHILLIPS,B.LUISI REVDAT 1 23-DEC-96 1IBE 0 JRNL AUTH J.WILSON,K.PHILLIPS,B.LUISI JRNL TITL THE CRYSTAL STRUCTURE OF HORSE DEOXYHAEMOGLOBIN JRNL TITL 2 TRAPPED IN THE HIGH-AFFINITY (R) STATE. JRNL REF J.MOL.BIOL. V. 264 743 1996 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 144335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2297 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.024 ; 0.025 REMARK 3 ANGLE DISTANCE (A) : 0.044 ; 0.035 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.051 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.018 ; 0.025 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.130 ; 0.120 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.190 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.290 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.190 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 3.060 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 20.440; 20.000 REMARK 3 TRANSVERSE (DEGREES) : 30.640; 30.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.337 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.532 ; 6.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.745 ; 8.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.006 ; 10.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IBE 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 (2007-05-31) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-1900 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : MULTIWIRE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD REMARK 200 DATA SCALING SOFTWARE : UCSD REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32227 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 1/2+X,1/2+Y,Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 54.09000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.59000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.09000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.59000 REMARK 290 SMTRY3 4 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 88.53137 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.92060 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O ALA B 140 ND1 HIS B 143 2.07 REMARK 500 O LEU A 73 O HOH 175 2.17 REMARK 500 O ALA B 142 ND1 HIS B 146 2.18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN B 2 75.75 148.73 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 59 DISTANCE = 5.32 ANGSTROMS REMARK 525 HOH 157 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH 171 DISTANCE = 5.66 ANGSTROMS REMARK 525 HOH 178 DISTANCE = 10.41 ANGSTROMS REMARK 525 HOH 179 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH 186 DISTANCE = 5.72 ANGSTROMS DBREF 1IBE A 1 141 UNP P01958 HBA_HORSE 1 141 DBREF 1IBE B 1 146 UNP P02062 HBB_HORSE 1 146 SEQADV 1IBE PHE A 24 UNP P01958 TYR 24 VARIANT SEQADV 1IBE ASP A 82 UNP P01958 ASN 82 CONFLICT SEQADV 1IBE ASN A 85 UNP P01958 ASP 85 CONFLICT 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 PHE 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 ASP LEU SER ASN 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 143 43 HET HEM B 147 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *187(H2 O) HELIX 1 1 ALA A 4 VAL A 17 1 14 HELIX 2 2 ALA A 21 GLY A 35 1 15 HELIX 3 3 PRO A 37 TYR A 42 5 6 HELIX 4 4 ALA A 53 GLY A 71 1 19 HELIX 5 5 LEU A 80 ALA A 88 1 9 HELIX 6 6 PRO A 95 HIS A 112 5 18 HELIX 7 7 PRO A 119 THR A 137 1 19 HELIX 8 8 GLY B 5 LYS B 17 1 13 HELIX 9 9 GLU B 20 VAL B 34 1 15 HELIX 10 10 PRO B 36 PHE B 41 5 6 HELIX 11 11 PRO B 51 GLY B 56 1 6 HELIX 12 12 PRO B 58 HIS B 77 1 20 HELIX 13 13 PHE B 85 CYS B 93 1 9 HELIX 14 14 ASP B 99 HIS B 117 5 19 HELIX 15 15 PRO B 124 ALA B 142 1 19 LINK FE HEM A 143 NE2 HIS A 87 LINK FE HEM B 147 NE2 HIS B 92 CRYST1 108.180 63.180 54.580 90.00 111.10 90.00 C 1 2 1 4 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 0.009244 0.000000 0.003567 0.00000 SCALE2 0.000000 0.015828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019638 0.00000