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HEADER OXYGEN TRANSPORT 24-JUN-98 4HBI TITLE SCAPHARCA DIMERIC HEMOGLOBIN, MUTANT T72I, DEOXY FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: SCAPHARCA DIMERIC HEMOGLOBIN, HEME GROUP, COMPND 7 PROTOPORPHYRIN IX IRON SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCAPHARCA INAEQUIVALVIS; SOURCE 3 ORGANISM_COMMON: ARK CLAM; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PGAP1 KEYWDS OXYGEN TRANSPORT, HEME, RESPIRATORY PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.E.ROYER JUNIOR REVDAT 2 01-APR-03 4HBI 1 JRNL REVDAT 1 11-NOV-98 4HBI 0 JRNL AUTH A.PARDANANI,A.GAMBACURTA,F.ASCOLI,W.E.ROYER JR. JRNL TITL MUTATIONAL DESTABILIZATION OF THE CRITICAL JRNL TITL 2 INTERFACE WATER CLUSTER IN SCAPHARCA DIMERIC JRNL TITL 3 HEMOGLOBIN: STRUCTURAL BASIS FOR ALTERED JRNL TITL 4 ALLOSTERIC ACTIVITY. JRNL REF J.MOL.BIOL. V. 284 729 1998 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.E.ROYER JUNIOR,A.PARDANANI,Q.H.GIBSON, REMARK 1 AUTH 2 E.S.PETERSON,J.M.FRIEDMAN REMARK 1 TITL ORDERED WATER MOLECULES AS KEY ALLOSTERIC REMARK 1 TITL 2 MEDIATORS IN A COOPERATIVE DIMERIC HEMOGLOBIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 93 14526 1996 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.GAMBACURTA,M.C.PIRO,M.COLETTA,M.E.CLEMENTI, REMARK 1 AUTH 2 F.POLIZIO,A.DESIDERI,R.SANTUCCI,F.ASCOLI REMARK 1 TITL A SINGLE MUTATION (THR72-->ILE) AT THE SUBUNIT REMARK 1 TITL 2 INTERFACE IS CRUCIAL FOR THE FUNCTIONAL PROPERTIES REMARK 1 TITL 3 OF THE HOMODIMERIC CO-OPERATIVE HAEMOGLOBIN FROM REMARK 1 TITL 4 SCAPHARCA INAEQUIVALVIS REMARK 1 REF J.MOL.BIOL. V. 248 910 1995 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH W.E.ROYER JUNIOR REMARK 1 TITL HIGH-RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A REMARK 1 TITL 2 CO-OPERATIVE DIMERIC HEMOGLOBIN REMARK 1 REF J.MOL.BIOL. V. 235 657 1994 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 32161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3615 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2234 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4HBI 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 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-1996 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU/MSC RU-H2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU REMARK 200 DATA SCALING SOFTWARE : RIGAKU REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.05600 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: ISOMORPHOUS MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: PDB ENTRY 4SDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 2.1M REMARK 280 NA/K PHOSPHATE AT PH 8.5 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 71.89500 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 71.89500 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 45.88000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.16000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.88000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.16000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.89500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.88000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 22.16000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.89500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.88000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 22.16000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 1 REMARK 465 PRO B 1 DBREF 4HBI A 1 146 UNP P02213 GLB1_SCAIN 1 146 DBREF 4HBI B 1 146 UNP P02213 GLB1_SCAIN 1 146 SEQADV 4HBI ILE A 72 UNP P02213 THR 72 ENGINEERED SEQADV 4HBI ILE B 72 UNP P02213 THR 72 ENGINEERED SEQRES 1 A 146 PRO SER VAL TYR ASP ALA ALA ALA GLN LEU THR ALA ASP SEQRES 2 A 146 VAL LYS LYS ASP LEU ARG ASP SER TRP LYS VAL ILE GLY SEQRES 3 A 146 SER ASP LYS LYS GLY ASN GLY VAL ALA LEU MET THR THR SEQRES 4 A 146 LEU PHE ALA ASP ASN GLN GLU THR ILE GLY TYR PHE LYS SEQRES 5 A 146 ARG LEU GLY ASP VAL SER GLN GLY MET ALA ASN ASP LYS SEQRES 6 A 146 LEU ARG GLY HIS SER ILE ILE LEU MET TYR ALA LEU GLN SEQRES 7 A 146 ASN PHE ILE ASP GLN LEU ASP ASN PRO ASP ASP LEU VAL SEQRES 8 A 146 CYS VAL VAL GLU LYS PHE ALA VAL ASN HIS ILE THR ARG SEQRES 9 A 146 LYS ILE SER ALA ALA GLU PHE GLY LYS ILE ASN GLY PRO SEQRES 10 A 146 ILE LYS LYS VAL LEU ALA SER LYS ASN PHE GLY ASP LYS SEQRES 11 A 146 TYR ALA ASN ALA TRP ALA LYS LEU VAL ALA VAL VAL GLN SEQRES 12 A 146 ALA ALA LEU SEQRES 1 B 146 PRO SER VAL TYR ASP ALA ALA ALA GLN LEU THR ALA ASP SEQRES 2 B 146 VAL LYS LYS ASP LEU ARG ASP SER TRP LYS VAL ILE GLY SEQRES 3 B 146 SER ASP LYS LYS GLY ASN GLY VAL ALA LEU MET THR THR SEQRES 4 B 146 LEU PHE ALA ASP ASN GLN GLU THR ILE GLY TYR PHE LYS SEQRES 5 B 146 ARG LEU GLY ASP VAL SER GLN GLY MET ALA ASN ASP LYS SEQRES 6 B 146 LEU ARG GLY HIS SER ILE ILE LEU MET TYR ALA LEU GLN SEQRES 7 B 146 ASN PHE ILE ASP GLN LEU ASP ASN PRO ASP ASP LEU VAL SEQRES 8 B 146 CYS VAL VAL GLU LYS PHE ALA VAL ASN HIS ILE THR ARG SEQRES 9 B 146 LYS ILE SER ALA ALA GLU PHE GLY LYS ILE ASN GLY PRO SEQRES 10 B 146 ILE LYS LYS VAL LEU ALA SER LYS ASN PHE GLY ASP LYS SEQRES 11 B 146 TYR ALA ASN ALA TRP ALA LYS LEU VAL ALA VAL VAL GLN SEQRES 12 B 146 ALA ALA LEU HET HEM A 153 43 HET HEM B 153 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *245(H2 O) HELIX 1 1 VAL A 3 GLN A 9 1 7 HELIX 2 2 ALA A 12 SER A 27 1 16 HELIX 3 3 LYS A 29 ASP A 43 1 15 HELIX 4 4 GLN A 45 LEU A 54 5 10 HELIX 5 5 VAL A 57 ALA A 62 5 6 HELIX 6 6 ASP A 64 GLN A 83 1 20 HELIX 7 7 PRO A 87 THR A 103 1 17 HELIX 8 8 ALA A 108 LYS A 125 1 18 HELIX 9 9 ASP A 129 ALA A 144 1 16 HELIX 10 10 VAL B 3 GLN B 9 1 7 HELIX 11 11 ALA B 12 SER B 27 1 16 HELIX 12 12 LYS B 29 ASP B 43 1 15 HELIX 13 13 GLN B 45 LEU B 54 5 10 HELIX 14 14 VAL B 57 ALA B 62 5 6 HELIX 15 15 ASP B 64 GLN B 83 1 20 HELIX 16 16 PRO B 87 THR B 103 1 17 HELIX 17 17 ALA B 108 LYS B 125 1 18 HELIX 18 18 ASP B 129 ALA B 144 1 16 LINK FE HEM A 153 NE2 HIS A 101 LINK FE HEM B 153 NE2 HIS B 101 CRYST1 91.760 44.320 143.790 90.00 90.00 90.00 C 2 2 21 16 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 0.010898 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006955 0.00000 MTRIX1 1 -0.351100 -0.320300 -0.879800 31.19000 1 MTRIX2 1 -0.309600 -0.847100 0.432000 12.99000 1 MTRIX3 1 -0.883700 0.424000 0.198200 18.27000 1