HEADER OXYGEN TRANSPORT 27-JUL-01 1GJN TITLE HYDROGEN PEROXIDE DERIVED MYOGLOBIN COMPOUND II AT PH 5.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: A FE(III)-BONDED HYDROXYL RADICAL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGAN: HEART KEYWDS REACTION INTERMEDIATE, HAEM, HEME, OXYGEN ACTIVATION, KEYWDS 2 PEROXIDASE, MONOOXYGENASE, FERRYL, HYDROXY RADICAL EXPDTA X-RAY DIFFRACTION AUTHOR H.-P.HERSLETH,B.DALHUS,C.H.GORBITZ,K.K.ANDERSSON REVDAT 2 01-APR-03 1GJN 1 JRNL REVDAT 1 01-MAR-02 1GJN 0 JRNL AUTH H.P.HERSLETH,B.DALHUS,C.H.GORBITZ,K.K.ANDERSSON JRNL TITL AN IRON HYDROXIDE MOIETY IN THE 1.35 A RESOLUTION JRNL TITL 2 STRUCTURE OF HYDROGEN PEROXIDE DERIVED MYOGLOBIN JRNL TITL 3 COMPOUND II AT PH 5.2. JRNL REF J.BIOL.INORG.CHEM. V. 7 299 2002 JRNL REFN ASTM JJBCFA GW ISSN 0949-8257 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.MAURUS,C.M.OVERALL,R.BOGUMIL,Y.LUO,A.G.MAUK, REMARK 1 AUTH 2 M.SMITH,G.D.BRAYER REMARK 1 TITL A MYOGLOBIN VARIANT WITH A POLAR SUBSTITUTION IN A REMARK 1 TITL 2 CONSERVED HYDROPHOBIC CLUSTER IN THE HEME BINDING REMARK 1 TITL 3 POCKET REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1341 1 1997 REMARK 1 REFN ASTM BBACAQ NE ISSN 0006-3002 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.SHERWOOD,A.G.MAUK,G.D.BRAYER REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DIFFRACTION DATA REMARK 1 TITL 2 FOR HORSE HEART METMYOGLOBIN REMARK 1 REF J.MOL.BIOL. V. 193 227 1987 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 25526 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) : 0.178 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1277 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3575 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 210 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1199 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.55000 REMARK 3 B22 (A**2) : 2.27000 REMARK 3 B33 (A**2) : 1.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : 0.15 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) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.11 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 : 0.44 REMARK 3 BSOL : 71.51 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 1GJN 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 (2007-05-31) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI . REMARK 100 THE EBI ID CODE IS EBI-8393 . REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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) : 0.8730 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 21.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1WLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 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 14.32500 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 MET A 131 SD MET A 131 CE -0.194 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. =-10.1 DEGREES REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 SITE_DESCRIPTION: SO4 BINDING SITE FOR CHAIN A DBREF 1GJN 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 HYD A1155 1 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM HYD HYDROXY GROUP HETSYN HEM HEME FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 HYD H O FORMUL 6 HOH *159(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 HYD A1155 LINK FE HEM A1154 NE2 HIS A 93 SITE 1 AC1 20 THR A 39 LYS A 42 PHE A 43 LYS A 45 SITE 2 AC1 20 HIS A 64 LEU A 89 SER A 92 HIS A 93 SITE 3 AC1 20 HIS A 97 ILE A 99 TYR A 103 HIS A 113 SITE 4 AC1 20 HIS A 116 GLN A 128 HOH Z 150 HOH Z 151 SITE 5 AC1 20 HOH Z 152 HOH Z 153 HOH Z 154 HOH Z 155 SITE 1 AC2 1 HIS A 64 SITE 1 AC3 3 THR A 51 GLU A 52 HOH Z 157 SITE 1 AC4 5 HIS A 81 HIS A 82 GLU A 83 HOH Z 158 SITE 2 AC4 5 HOH Z 159 CRYST1 62.862 28.650 35.352 90.00 105.93 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 0.015908 0.000000 0.004540 0.00000 SCALE2 0.000000 0.034904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029417 0.00000