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HEADER OXYGEN TRANSPORT 26-MAR-99 1CG5 TITLE DEOXY FORM HEMOGLOBIN FROM DASYATIS AKAJEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HEMOGLOBIN); COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: PROTEIN (HEMOGLOBIN); COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DASYATIS AKAJEI; SOURCE 3 ORGANISM_COMMON: AKAEI; SOURCE 4 CELL: ERYTHROCYTE; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: DASYATIS AKAJEI; SOURCE 7 ORGANISM_COMMON: AKAEI; SOURCE 8 CELL: ERYTHROCYTE KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR K.T.CHONG,H.MORIMOTO REVDAT 4 01-APR-03 1CG5 1 JRNL REVDAT 3 03-NOV-99 1CG5 1 JRNL REMARK REVDAT 2 01-SEP-99 1CG5 1 JRNL REVDAT 1 01-APR-99 1CG5 0 JRNL AUTH K.T.CHONG,G.MIYAZAKI,H.MORIMOTO,Y.ODA,S.Y.PARK JRNL TITL STRUCTURES OF THE DEOXY AND CO FORMS OF JRNL TITL 2 HAEMOGLOBIN FROM DASYATIS AKAJEI, A CARTILAGINOUS JRNL TITL 3 FISH. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 55 1291 1999 JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 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) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 41888 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) : 0.191 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2138 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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 : 2272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.70 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.19 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) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.840 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.060 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.730 ; 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 : PARHCSDX.PRO 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 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CG5 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 (2007-05-01) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB000741. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42219 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.06800 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 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: 2HHB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+Z REMARK 290 4555 -Y,-X,2/3-Z REMARK 290 5555 -X+Y,Y,1/3-Z REMARK 290 6555 X,X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.10667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.21333 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 66.21333 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.10667 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.10667 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 52 CB CYS A 52 SG 0.043 REMARK 500 HIS A 88 CG HIS A 88 CD2 0.059 REMARK 500 HIS B 88 CG HIS B 88 CD2 0.050 REMARK 500 MET B 106 CG MET B 106 SD -0.058 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 ASN A 113 N - CA - C ANGL. DEV. = 8.4 DEGREES REMARK 500 SER A 138 N - CA - C ANGL. DEV. = 9.3 DEGREES REMARK 500 ASP B 19 N - CA - C ANGL. DEV. = -7.5 DEGREES REMARK 500 PHE B 49 N - CA - C ANGL. DEV. = 7.3 DEGREES REMARK 500 SER B 138 N - CA - C ANGL. DEV. = 7.3 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 44 DISTANCE = 6.81 ANGSTROMS DBREF 1CG5 A 1 141 UNP P56691 HBA_DASAK 2 142 DBREF 1CG5 B 1 141 UNP P56692 HBB_DASAK 2 142 SEQRES 1 A 141 VAL LEU SER SER GLN ASN LYS LYS ALA ILE GLU GLU LEU SEQRES 2 A 141 GLY ASN LEU ILE LYS ALA ASN ALA GLU ALA TRP GLY ALA SEQRES 3 A 141 ASP ALA LEU ALA ARG LEU PHE GLU LEU HIS PRO GLN THR SEQRES 4 A 141 LYS THR TYR PHE SER LYS PHE SER GLY PHE GLU ALA CYS SEQRES 5 A 141 ASN GLU GLN VAL LYS LYS HIS GLY LYS ARG VAL MET ASN SEQRES 6 A 141 ALA LEU ALA ASP ALA THR HIS HIS LEU ASP ASN LEU HIS SEQRES 7 A 141 LEU HIS LEU GLU ASP LEU ALA ARG LYS HIS GLY GLU ASN SEQRES 8 A 141 LEU LEU VAL ASP PRO HIS ASN PHE HIS LEU PHE ALA ASP SEQRES 9 A 141 CYS ILE VAL VAL THR LEU ALA VAL ASN LEU GLN ALA PHE SEQRES 10 A 141 THR PRO VAL THR HIS CYS ALA VAL ASP LYS PHE LEU GLU SEQRES 11 A 141 LEU VAL ALA TYR GLU LEU SER SER CYS TYR ARG SEQRES 1 B 141 VAL LYS LEU SER GLU ASP GLN GLU HIS TYR ILE LYS GLY SEQRES 2 B 141 VAL TRP LYS ASP VAL ASP HIS LYS GLN ILE THR ALA LYS SEQRES 3 B 141 ALA LEU GLU ARG VAL PHE VAL VAL TYR PRO TRP THR THR SEQRES 4 B 141 ARG LEU PHE SER LYS LEU GLN GLY LEU PHE SER ALA ASN SEQRES 5 B 141 ASP ILE GLY VAL GLN GLN HIS ALA ASP LYS VAL GLN ARG SEQRES 6 B 141 ALA LEU GLY GLU ALA ILE ASP ASP LEU LYS LYS VAL GLU SEQRES 7 B 141 ILE ASN PHE GLN ASN LEU SER GLY LYS HIS GLN GLU ILE SEQRES 8 B 141 GLY VAL ASP THR GLN ASN PHE LYS LEU LEU GLY GLN THR SEQRES 9 B 141 PHE MET VAL GLU LEU ALA LEU HIS TYR LYS LYS THR PHE SEQRES 10 B 141 ARG PRO LYS GLU HIS ALA ALA ALA TYR LYS PHE PHE ARG SEQRES 11 B 141 LEU VAL ALA GLU ALA LEU SER SER ASN TYR HIS HET HEM A 142 43 HET HEM B 142 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *151(H2 O) HELIX 1 1 SER A 4 LEU A 35 1 32 HELIX 2 2 PRO A 37 TYR A 42 5 6 HELIX 3 3 GLU A 54 HIS A 72 1 19 HELIX 4 4 LEU A 77 HIS A 80 1 4 HELIX 5 5 GLU A 82 GLU A 90 1 9 HELIX 6 6 PRO A 96 ASN A 113 5 18 HELIX 7 7 PRO A 119 SER A 137 1 19 HELIX 8 8 GLU B 5 ASP B 17 1 13 HELIX 9 9 HIS B 20 VAL B 34 1 15 HELIX 10 10 PRO B 36 THR B 39 5 4 HELIX 11 11 SER B 43 LEU B 45 5 3 HELIX 12 12 ILE B 54 ASP B 73 1 20 HELIX 13 13 VAL B 77 ASN B 80 1 4 HELIX 14 14 GLN B 82 ILE B 91 1 10 HELIX 15 15 THR B 95 THR B 116 5 22 HELIX 16 16 PRO B 119 SER B 137 1 19 LINK NE2 HIS A 88 FE HEM A 142 LINK NE2 HIS B 88 FE HEM B 142 CRYST1 77.760 77.760 99.320 90.00 90.00 120.00 P 31 1 2 6 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 0.012860 0.007425 0.000000 0.00000 SCALE2 0.000000 0.014849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010068 0.00000