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HEADER OXYGEN STORAGE/TRANSPORT 23-NOV-03 1V5H TITLE CRYSTAL STRUCTURE OF HUMAN CYTOGLOBIN (FERRIC FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTOGLOBIN, HGB, STELLATE CELL ACTIVATION- COMPND 5 ASSOCIATED PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: CYGB, STAP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS GLOBIN, HEME, OXYGEN TRANSPORT, OXYGEN STORAGE, LIGAND KEYWDS 2 BINDING, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 3 RSGI, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR H.SUGIMOTO,M.MAKINO,H.SAWAI,N.KAWADA,K.YOSHIZATO,Y.SHIRO, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 1 08-JUN-04 1V5H 0 JRNL AUTH H.SUGIMOTO,M.MAKINO,H.SAWAI,N.KAWADA,K.YOSHIZATO, JRNL AUTH 2 Y.SHIRO JRNL TITL STRUCTURAL BASIS OF HUMAN CYTOGLOBIN FOR LIGAND JRNL TITL 2 BINDING. JRNL REF J.MOL.BIOL. V. 339 873 2004 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.SAWAI,N.KAWADA,K.YOSHIZATO,H.NAKAJIMA,S.AONO, REMARK 1 AUTH 2 Y.SHIRO REMARK 1 TITL CHARACTERIZATION OF THE HEME ENVIRONMENTAL REMARK 1 TITL 2 STRUCTURE OF CYTOGLOBIN, A FOURTH GLOBIN IN HUMANS REMARK 1 REF BIOCHEMISTRY V. 42 5133 2003 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 761175.430 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 7331 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) : 0.248 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 384 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 896 REMARK 3 BIN R VALUE (WORKING SET) : 0.3720 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 52 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.057 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1220 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.31000 REMARK 3 B22 (A**2) : 11.63000 REMARK 3 B33 (A**2) : -17.95000 REMARK 3 B12 (A**2) : 4.67000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 2.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.32 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 62.53 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V5H 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 (2007-03-17) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ . REMARK 100 THE RCSB ID CODE IS RCSB006230. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-2003 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0, 1.7409, 1.7394, 1.7364, REMARK 200 1.7432 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7348 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28900 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 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): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, CHES, PH 9.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,2/3+Z REMARK 290 3555 -X+Y,-X,1/3+Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,1/3-Z REMARK 290 6555 -X,-X+Y,2/3-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 39.75600 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 19.87800 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 0.00000 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 19.87800 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 39.75600 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 1 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 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 -0.500000 -0.866025 0.000000 111.60150 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 64.43316 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -19.87800 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 LYS A 3 REMARK 465 VAL A 4 REMARK 465 PRO A 5 REMARK 465 GLY A 6 REMARK 465 GLU A 7 REMARK 465 MET A 8 REMARK 465 GLU A 9 REMARK 465 ILE A 10 REMARK 465 GLU A 11 REMARK 465 ARG A 12 REMARK 465 ARG A 13 REMARK 465 GLU A 14 REMARK 465 ARG A 15 REMARK 465 SER A 16 REMARK 465 GLU A 17 REMARK 465 GLU A 18 REMARK 465 LEU A 19 REMARK 465 SER A 20 REMARK 465 VAL A 172 REMARK 465 GLN A 173 REMARK 465 GLN A 174 REMARK 465 VAL A 175 REMARK 465 PRO A 176 REMARK 465 ASN A 177 REMARK 465 ALA A 178 REMARK 465 THR A 179 REMARK 465 THR A 180 REMARK 465 PRO A 181 REMARK 465 PRO A 182 REMARK 465 ALA A 183 REMARK 465 THR A 184 REMARK 465 LEU A 185 REMARK 465 PRO A 186 REMARK 465 SER A 187 REMARK 465 SER A 188 REMARK 465 GLY A 189 REMARK 465 PRO A 190 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 PHE A 139 CB - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 PHE A 139 N - CA - C ANGL. DEV. =-13.5 DEGREES REMARK 500 SER A 141 N - CA - C ANGL. DEV. =-20.5 DEGREES REMARK 500 PRO A 144 N - CA - C ANGL. DEV. = 21.1 DEGREES REMARK 500 PRO A 144 C - N - CA ANGL. DEV. = 15.7 DEGREES REMARK 500 PRO A 144 C - N - CD ANGL. DEV. =-14.2 DEGREES REMARK 500 PRO A 145 C - N - CA ANGL. DEV. = 14.9 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MY_001000023.2 RELATED DB: TARGETDB DBREF 1V5H A 1 190 UNP Q8WWM9 CYGB_HUMAN 1 190 SEQADV 1V5H GLY A -2 UNP Q8WWM9 CLONING ARTIFACT SEQADV 1V5H SER A -1 UNP Q8WWM9 CLONING ARTIFACT SEQADV 1V5H HIS A 0 UNP Q8WWM9 CLONING ARTIFACT SEQRES 1 A 193 GLY SER HIS MET GLU LYS VAL PRO GLY GLU MET GLU ILE SEQRES 2 A 193 GLU ARG ARG GLU ARG SER GLU GLU LEU SER GLU ALA GLU SEQRES 3 A 193 ARG LYS ALA VAL GLN ALA MET TRP ALA ARG LEU TYR ALA SEQRES 4 A 193 ASN CYS GLU ASP VAL GLY VAL ALA ILE LEU VAL ARG PHE SEQRES 5 A 193 PHE VAL ASN PHE PRO SER ALA LYS GLN TYR PHE SER GLN SEQRES 6 A 193 PHE LYS HIS MET GLU ASP PRO LEU GLU MET GLU ARG SER SEQRES 7 A 193 PRO GLN LEU ARG LYS HIS ALA CYS ARG VAL MET GLY ALA SEQRES 8 A 193 LEU ASN THR VAL VAL GLU ASN LEU HIS ASP PRO ASP LYS SEQRES 9 A 193 VAL SER SER VAL LEU ALA LEU VAL GLY LYS ALA HIS ALA SEQRES 10 A 193 LEU LYS HIS LYS VAL GLU PRO VAL TYR PHE LYS ILE LEU SEQRES 11 A 193 SER GLY VAL ILE LEU GLU VAL VAL ALA GLU GLU PHE ALA SEQRES 12 A 193 SER ASP PHE PRO PRO GLU THR GLN ARG ALA TRP ALA LYS SEQRES 13 A 193 LEU ARG GLY LEU ILE TYR SER HIS VAL THR ALA ALA TYR SEQRES 14 A 193 LYS GLU VAL GLY TRP VAL GLN GLN VAL PRO ASN ALA THR SEQRES 15 A 193 THR PRO PRO ALA THR LEU PRO SER SER GLY PRO HET HEM A 191 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *30(H2 O) HELIX 1 1 ALA A 22 TYR A 35 1 14 HELIX 2 2 ASP A 40 PHE A 53 1 14 HELIX 3 3 PRO A 54 GLN A 58 5 5 HELIX 4 4 ASP A 68 SER A 75 1 8 HELIX 5 5 SER A 75 ASN A 95 1 21 HELIX 6 6 ASP A 98 LYS A 116 1 19 HELIX 7 7 PRO A 121 PHE A 139 1 19 HELIX 8 8 GLU A 146 GLY A 170 1 25 LINK FE HEM A 191 NE2 HIS A 81 LINK FE HEM A 191 NE2 HIS A 113 CRYST1 74.401 74.401 59.634 90.00 90.00 120.00 P 32 2 1 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 0.013441 0.007760 0.000000 0.00000 SCALE2 0.000000 0.015520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016769 0.00000