[Scop | Full Entry | Seq (local cached copy) | More Options ]
HEADER OXYGEN TRANSPORT 24-MAY-07 2V1H TITLE CRYSTAL STRUCTURE OF RADIATION-INDUCED METMYOGLOBIN- AQUA TITLE 2 FERROUS MYOGLOBIN AT PH 5.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: FE(II)-OH2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGAN: HEART KEYWDS OXYGEN TRANSPORT, OXYGEN ACTIVATION, RADIATION, KEYWDS 2 MONOOXYGENASE, METAL-BINDING, MUSCLE PROTEIN, REACTION KEYWDS 3 INTERMEDIATE, IRON, HEME, TRANSPORT, HAEM EXPDTA X-RAY DIFFRACTION AUTHOR H.-P.HERSLETH,C.H.GORBITZ,K.K.ANDERSSON REVDAT 1 12-JUN-07 2V1H 0 JRNL AUTH H.-P.HERSLETH,T.UCHIDA,A.K.ROHR,T.TESCHNER, JRNL AUTH 2 V.SCHUNEMANN,T.KITAGAWA,A.X.TRAUTWEIN,C.H.GORBITZ, JRNL AUTH 3 K.K.ANDERSSON JRNL TITL CRYSTALLOGRAPHIC AND SPECTROSCOPICAL STUDIES OF JRNL TITL 2 PEROXIDE-DERIVED MYOGLOBIN COMPOUND II. OCCURRENCE JRNL TITL 3 OF PROTONATED FE(IV)O JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 28240 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 + TEST SET) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1493 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : NULL REMARK 3 BIN RESOLUTION RANGE LOW : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : 2064 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1540 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.1980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 1502 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : 0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.056 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.542 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1370 ; 0.054 ; 0.054 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1827 ; 0.975 ; 2.019 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 167 ; 4.128 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 54 ;34.456 ;25.185 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 248 ;10.936 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;17.316 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 191 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 985 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 708 ; 0.228 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 906 ; 0.327 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 240 ; 0.186 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 69 ; 0.185 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 59 ; 0.248 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 796 ; 1.940 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1248 ; 2.737 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 618 ; 2.299 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 571 ; 3.299 ; 3.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 0 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2V1H 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 (2007-06-08) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI. REMARK 100 THE EBI ID CODE IS EBI-32658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-2003 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 5.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8727 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.520 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.26 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.750 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1GJN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BATCH METHOD: 6-12 MG/ML MYOGLOBIN, REMARK 280 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM REMARK 280 SULPHATE, 5-10% OF GLYCEROL PH 5.2) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -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 14.34400 REMARK 290 SMTRY3 2 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 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, Z 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 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 GLY A 1 N GLY A 1 CA 0.041 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 123 N - CA - C ANGL. DEV. = -6.7 DEGREES REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 SITE_DESCRIPTION: GOL BINDING SITE FOR CHAIN A DBREF 2V1H A 1 153 UNP P68082 MYG_HORSE 1 153 SEQRES 1 A 153 GLY LEU SER ASP GLY GLU TRP GLN GLN VAL LEU ASN VAL SEQRES 2 A 153 TRP GLY LYS VAL GLU ALA ASP ILE ALA GLY HIS GLY GLN SEQRES 3 A 153 GLU VAL LEU ILE ARG LEU PHE THR GLY HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP LYS PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 153 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 153 THR VAL VAL LEU THR ALA LEU GLY GLY ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER ASP ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 153 LYS HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET THR LYS ALA LEU GLU LEU PHE ARG ASN ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY PHE GLN GLY HET SO4 A1156 5 HET SO4 A1157 5 HET HEM A1154 43 HET GOL A1158 6 HET GOL A1159 6 HET GOL A1160 6 HET GOL A1161 6 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETSYN HEM HEME FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 GOL 4(C3 H8 O3) FORMUL 9 HOH *184(H2 O) HELIX 1 1 SER A 3 ALA A 19 1 17 HELIX 2 2 ASP A 20 HIS A 36 1 17 HELIX 3 3 HIS A 36 GLU A 41 1 6 HELIX 4 4 THR A 51 SER A 58 1 8 HELIX 5 5 SER A 58 LYS A 77 1 20 HELIX 6 6 HIS A 82 LYS A 96 1 15 HELIX 7 7 PRO A 100 HIS A 119 1 20 HELIX 8 8 GLY A 124 GLY A 150 1 27 LINK FE HEM A1154 O HOH A1155 LINK FE HEM A1154 NE2 HIS A 93 SITE 1 AC1 22 THR A 39 LYS A 42 PHE A 43 LYS A 45 SITE 2 AC1 22 HIS A 64 LEU A 89 SER A 92 HIS A 93 SITE 3 AC1 22 HIS A 97 ILE A 99 TYR A 103 LEU A 104 SITE 4 AC1 22 HIS A 113 HIS A 116 GLN A 128 HOH A1155 SITE 5 AC1 22 HOH Z 168 HOH Z 169 HOH Z 170 HOH Z 171 SITE 6 AC1 22 HOH Z 172 HOH Z 174 SITE 1 AC2 6 THR A 51 GLU A 52 HOH Z 175 HOH Z 177 SITE 2 AC2 6 HOH Z 178 HOH Z 179 SITE 1 AC3 4 GLY A 1 HOH Z 180 HOH Z 181 HOH Z 182 SITE 1 AC4 6 LYS A 45 LYS A 63 HIS A 64 SER A 117 SITE 2 AC4 6 HOH Z 168 HOH Z 183 SITE 1 AC5 7 LYS A 45 ASP A 60 LYS A 63 HIS A 113 SITE 2 AC5 7 SER A 117 HOH Z 38 HOH Z 42 SITE 1 AC6 2 ASP A 20 HOH Z 26 SITE 1 AC7 3 SER A 3 GLY A 5 HOH Z 11 CRYST1 63.192 28.688 35.557 90.00 105.81 90.00 P 1 21 1 2 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 0.015825 0.000000 0.004481 0.00000 SCALE2 0.000000 0.034858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029230 0.00000