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HEADER OXYGEN TRANSPORT 29-JAN-98 1A4F TITLE BAR-HEADED GOOSE HEMOGLOBIN (OXY FORM) 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: ANSER INDICUS; SOURCE 3 ORGANISM_COMMON: BAR-HEADED GOOSE; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ANSER INDICUS; SOURCE 6 ORGANISM_COMMON: BAR-HEADED GOOSE KEYWDS OXYGEN TRANSPORT, HEME, RESPIRATORY PROTEIN, ERYTHROCYTE EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,X.GU REVDAT 1 29-APR-98 1A4F 0 JRNL AUTH J.ZHANG,Z.HUA,J.R.TAME,G.LU,R.ZHANG,X.GU JRNL TITL THE CRYSTAL STRUCTURE OF A HIGH OXYGEN AFFINITY JRNL TITL 2 SPECIES OF HAEMOGLOBIN (BAR-HEADED GOOSE JRNL TITL 3 HAEMOGLOBIN IN THE OXY FORM). JRNL REF J.MOL.BIOL. V. 255 484 1996 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.1 REMARK 3 NUMBER OF REFLECTIONS : 2488 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) : 0.198 REMARK 3 FREE R VALUE : NULL 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 : 2250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.40 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.019 ; 0.015 REMARK 3 ANGLE DISTANCE (A) : 0.052 ; 0.025 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.075 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.263 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.223 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.260 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.000 ; 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) : 2.990 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 24.100; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 39.700; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 5.888 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.412 ; 6.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 10.390; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.070; 10.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE OVERALL GEOMETRY IS RELATIVELY REMARK 3 POOR. REMARK 4 REMARK 4 1A4F 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 3.100 (2007-03-16) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-1992 REMARK 200 TEMPERATURE (KELVIN) : 283.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : FILM REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : WEIS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24887 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.05100 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: AUTOMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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-Y,1/2+X,1/2+Z REMARK 290 4555 1/2+Y,1/2-X,1/2+Z REMARK 290 5555 1/2-X,1/2+Y,1/2-Z REMARK 290 6555 1/2+X,1/2-Y,1/2-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 40.79500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.64000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.79500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.79500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.64000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.79500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.79500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.64000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.79500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.79500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.64000 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 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 81.59000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 LYS A 82 CA - CB - CG ANGL. DEV. = 26.6 DEGREES 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 LEU A 2 113.78 25.75 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 14 DISTANCE = 5.40 ANGSTROMS REMARK 525 HOH 35 DISTANCE = 6.12 ANGSTROMS DBREF 1A4F A 1 141 UNP P01990 HBA_ANSIN 1 141 DBREF 1A4F B 1 146 UNP P02118 HBB_ANSIN 1 146 SEQRES 1 A 141 VAL LEU SER ALA ALA ASP LYS THR ASN VAL LYS GLY VAL SEQRES 2 A 141 PHE SER LYS ILE SER GLY HIS ALA GLU GLU TYR GLY ALA SEQRES 3 A 141 GLU THR LEU GLU ARG MET PHE THR ALA TYR PRO GLN THR SEQRES 4 A 141 LYS THR TYR PHE PRO HIS PHE ASP LEU GLN HIS GLY SER SEQRES 5 A 141 ALA GLN ILE LYS ALA HIS GLY LYS LYS VAL VAL ALA ALA SEQRES 6 A 141 LEU VAL GLU ALA VAL ASN HIS ILE ASP ASP ILE ALA GLY SEQRES 7 A 141 ALA LEU SER LYS LEU SER ASP LEU HIS ALA GLN LYS LEU SEQRES 8 A 141 ARG VAL ASP PRO VAL ASN PHE LYS PHE LEU GLY HIS CYS SEQRES 9 A 141 PHE LEU VAL VAL VAL ALA ILE HIS HIS PRO SER ALA LEU SEQRES 10 A 141 THR ALA GLU VAL HIS ALA SER LEU ASP LYS PHE LEU CYS SEQRES 11 A 141 ALA VAL GLY THR VAL LEU THR ALA LYS TYR ARG SEQRES 1 B 146 VAL HIS TRP SER ALA GLU GLU LYS GLN LEU ILE THR GLY SEQRES 2 B 146 LEU TRP GLY LYS VAL ASN VAL ALA ASP CYS GLY ALA GLU SEQRES 3 B 146 ALA LEU ALA ARG LEU LEU ILE VAL TYR PRO TRP THR GLN SEQRES 4 B 146 ARG PHE PHE SER SER PHE GLY ASN LEU SER SER PRO THR SEQRES 5 B 146 ALA ILE LEU GLY ASN PRO MET VAL ARG ALA HIS GLY LYS SEQRES 6 B 146 LYS VAL LEU THR SER PHE GLY ASP ALA VAL LYS ASN LEU SEQRES 7 B 146 ASP ASN ILE LYS ASN THR PHE ALA GLN 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 ASP ILE LEU ILE ILE VAL LEU ALA ALA HIS SEQRES 10 B 146 PHE ALA LYS GLU PHE THR PRO ASP CYS GLN ALA ALA TRP SEQRES 11 B 146 GLN LYS LEU VAL ARG VAL VAL ALA HIS ALA LEU ALA ARG SEQRES 12 B 146 LYS TYR HIS HET HEM A 150 43 HET OXY A 150 2 HET HEM B 150 43 HET OXY B 150 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 OXY 2(O2) FORMUL 7 HOH *108(H2 O) HELIX 1 1 ALA A 4 ILE A 17 1 14 HELIX 2 2 ALA A 21 ALA A 35 1 15 HELIX 3 3 PRO A 37 TYR A 42 5 6 HELIX 4 4 ALA A 53 VAL A 70 1 18 HELIX 5 5 ILE A 76 ALA A 88 1 13 HELIX 6 6 PRO A 95 HIS A 112 5 18 HELIX 7 7 ALA A 119 VAL A 135 1 17 HELIX 8 8 ALA B 5 LYS B 17 1 13 HELIX 9 9 VAL B 20 VAL B 34 1 15 HELIX 10 10 PRO B 36 PHE B 45 5 10 HELIX 11 11 PRO B 51 LEU B 55 1 5 HELIX 12 12 PRO B 58 LYS B 76 1 19 HELIX 13 13 ILE B 81 ASP B 94 1 14 HELIX 14 14 PRO B 100 GLU B 121 1 22 HELIX 15 15 PRO B 124 ALA B 142 1 19 LINK FE HEM A 150 NE2 HIS A 87 LINK FE HEM A 150 O1 OXY A 150 LINK FE HEM B 150 NE2 HIS B 92 LINK FE HEM B 150 O1 OXY B 150 CRYST1 81.590 81.590 107.280 90.00 90.00 90.00 P 42 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 0.012256 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009321 0.00000