HEADER OXYGEN TRANSPORT 13-MAR-97 3HBI OBSLTE 28-MAR-06 3HBI 2AV0 TITLE MUTATION OF RESIDUE PHE 97 TO LEU DISRUPTS THE CENTRAL TITLE 2 ALLOSTERIC PATHWAY OF SCAPHARCA DIMERIC HEMOGLOBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCAPHARCA DIMERIC HEMOGLOBIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HBI; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: SCAPHARCA DIMERIC HEMOGLOBIN, CO-LIGANDED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCAPHARCA INAEQUIVALVIS; SOURCE 3 ORGANISM_COMMON: ARK CLAM; SOURCE 4 GENE: HBI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: W3110LACIQ L8; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCS-26; SOURCE 10 EXPRESSION_SYSTEM_GENE: HBI; SOURCE 11 OTHER_DETAILS: SYNTHETIC GENE KEYWDS HEMOGLOBIN, HEME, OXYGEN TRANSPORT, RESPIRATORY PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.PARDANANI,W.E.ROYER JUNIOR REVDAT 2 01-APR-03 3HBI 1 JRNL REVDAT 1 20-AUG-97 3HBI 0 JRNL AUTH A.PARDANANI,Q.H.GIBSON,G.COLOTTI,W.E.ROYER JR. JRNL TITL MUTATION OF RESIDUE PHE97 TO LEU DISRUPTS THE JRNL TITL 2 CENTRAL ALLOSTERIC PATHWAY IN SCAPHARCA DIMERIC JRNL TITL 3 HEMOGLOBIN. JRNL REF J.BIOL.CHEM. V. 272 13171 1997 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 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) (%) : 88.8 REMARK 3 NUMBER OF REFLECTIONS : 40595 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) : 0.186 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2226 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.70 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.50 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 16.700; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 19.200; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : PARAM19X.HEME REMARK 3 PARAMETER FILE 3 : PARAM19.SOL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19X.HEME REMARK 3 TOPOLOGY FILE 3 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HBI COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-01) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-1995 REMARK 200 TEMPERATURE (KELVIN) : 300.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 2 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 : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : R-AXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40595 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05520 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.843 REMARK 200 STARTING MODEL: PDB ENTRY 3SDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 - 50 MG/ML HEMOGLOBIN; 1.9 - 2.2 REMARK 280 M PHOSPHATE BUFFER, PH 7.5 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 46.62500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.62500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.99000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 295 REMARK 295 NON-CRYSTALLOGRAPHIC SYMMETRY REMARK 295 THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW REMARK 295 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS REMARK 295 IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX REMARK 295 TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD REMARK 295 APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. REMARK 295 CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH REMARK 295 ATOMS ARE NOT FOUND IN THIS ENTRY. REMARK 295 REMARK 295 APPLIED TO TRANSFORMED TO REMARK 295 TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD REMARK 295 SSS REMARK 295 M 1 A 2 .. 146 B 2 .. 146 0.419 REMARK 295 REMARK 295 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK 295 REMARK 295 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 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 3SDH REMARK 999 REMARK 999 SEQUENCE REMARK 999 3HBI A SWS P02213 1 - 1 NOT IN ATOMS LIST REMARK 999 3HBI B SWS P02213 1 - 1 NOT IN ATOMS LIST DBREF 3HBI A 1 146 UNP P02213 GLB1_SCAIN 1 146 DBREF 3HBI B 1 146 UNP P02213 GLB1_SCAIN 1 146 SEQADV 3HBI ASN A 56 UNP P02213 ASP 56 ENGINEERED SEQADV 3HBI LEU A 97 UNP P02213 PHE 97 ENGINEERED SEQADV 3HBI ASN B 56 UNP P02213 ASP 56 ENGINEERED SEQADV 3HBI LEU B 97 UNP P02213 PHE 97 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 ASN VAL SER GLN GLY MET ALA ASN ASP LYS SEQRES 6 A 146 LEU ARG GLY HIS SER ILE THR 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 LEU 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 ASN VAL SER GLN GLY MET ALA ASN ASP LYS SEQRES 6 B 146 LEU ARG GLY HIS SER ILE THR 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 LEU 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 47 HET CMO A 154 2 HET HEM B 153 47 HET CMO B 154 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 *222(H2 O) HELIX 1 PRA VAL A 3 GLN A 9 1 7 HELIX 2 AA ALA A 12 ILE A 25 1 14 HELIX 3 BA LYS A 29 ASP A 43 1 15 HELIX 4 CA GLN A 45 TYR A 50 5 6 HELIX 5 EA ASP A 64 ASP A 82 1 19 HELIX 6 FA PRO A 87 THR A 103 1 17 HELIX 7 GA ALA A 108 SER A 124 1 17 HELIX 8 HA ASP A 129 ALA A 144 1 16 HELIX 9 PRB VAL B 3 GLN B 9 1 7 HELIX 10 AB ALA B 12 ILE B 25 1 14 HELIX 11 BB LYS B 29 ASP B 43 1 15 HELIX 12 CB GLN B 45 TYR B 50 5 6 HELIX 13 EB ASP B 64 ASP B 82 1 19 HELIX 14 FB PRO B 87 THR B 103 1 17 HELIX 15 GB ALA B 108 SER B 124 1 17 HELIX 16 HB ASP B 129 ALA B 144 1 16 LINK FE HEM A 153 NE2 HIS A 101 LINK FE HEM A 153 C CMO A 154 LINK FE HEM B 153 NE2 HIS B 101 LINK FE HEM B 153 C CMO B 154 CRYST1 93.250 43.980 83.500 90.00 122.03 90.00 C 1 2 1 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 0.010724 0.000000 0.006709 0.00000 SCALE2 0.000000 0.022738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014127 0.00000 MTRIX1 1 -0.336300 -0.269500 -0.902400 60.83000 1 MTRIX2 1 -0.257800 -0.895300 0.363400 2.57000 1 MTRIX3 1 -0.905800 0.354800 0.231600 43.88000 1