HEADER OXIDOREDUCTASE 08-JUL-01 1H7K TITLE FORMATION OF A TYROSYL RADICAL INTERMEDIATE IN PROTEUS MIRABILIS TITLE 2 CATALASE BY DIRECTED MUTAGENESIS AND CONSEQUENCES FOR NUCLEOTIDE TITLE 3 REACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.6; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: METHIONINE SULFONE IN POSITION 53, TYROSINE 337 LACK COMPND 7 THE HYDROXYL HYDROGEN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEUS MIRABILIS; SOURCE 3 ORGANISM_TAXID: 584; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109 DE3; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PALTER-CAT-F215Y KEYWDS OXIDOREDUCTASE, OXIDOREDUCTASE (H2O2 ACCEPTOR), PEROXIDASE, IRON, KEYWDS 2 HEM, HYDROGEN PEROXIDE, NADP EXPDTA X-RAY DIFFRACTION AUTHOR P.ANDREOLETTI,S.GAMBARELLI,J.GAILLARD,G.SAINZ,V.STOJANOFF,H.M.JOUVE REVDAT 7 23-OCT-24 1H7K 1 REMARK REVDAT 6 13-DEC-23 1H7K 1 REMARK SHEET LINK REVDAT 5 08-MAY-19 1H7K 1 REMARK REVDAT 4 03-APR-19 1H7K 1 REMARK LINK REVDAT 3 16-SEP-15 1H7K 1 COMPND SOURCE KEYWDS AUTHOR REVDAT 3 2 1 JRNL REMARK VERSN HETSYN REVDAT 3 3 1 FORMUL HELIX SHEET MASTER REVDAT 2 24-FEB-09 1H7K 1 VERSN REVDAT 1 25-FEB-04 1H7K 0 JRNL AUTH P.ANDREOLETTI,S.GAMBARELLI,G.SAINZ,V.STOJANOFF,C.WHITE, JRNL AUTH 2 G.DESFONDS,J.GAGNON,J.GAILLARD,H.M.JOUVE JRNL TITL FORMATION OF A TYROSYL RADICAL INTERMEDIATE IN PROTEUS JRNL TITL 2 MIRABILIS CATALASE BY DIRECTED MUTAGENESIS AND CONSEQUENCES JRNL TITL 3 FOR NUCLEOTIDE REACTIVITY. JRNL REF BIOCHEMISTRY V. 40 13734 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11695923 JRNL DOI 10.1021/BI010687F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.GOUET,H.M.JOUVE,P.A.WILLIAMS,I.ANDERSSON,P.ANDREOLETTI, REMARK 1 AUTH 2 L.NUSSAUME,J.HAJDU REMARK 1 TITL FERRYL INTERMEDIATES OF CATALASE CAPTURED BY TIME-RESOLVED REMARK 1 TITL 2 WEISSENBERG CRYSTALLOGRAPHY AND UV-VIS SPECTROSCOPY REMARK 1 REF NAT.STRUCT.BIOL. V. 3 951 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 8901874 REMARK 1 DOI 10.1038/NSB1196-951 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.GOUET,H.M.JOUVE,O.DIDEBERG REMARK 1 TITL CRYSTAL STRUCTURE OF PROTEUS MIRABILIS PR CATALASE WITH AND REMARK 1 TITL 2 WITHOUT BOUND NADPH REMARK 1 REF J.MOL.BIOL. V. 249 933 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7791219 REMARK 1 DOI 10.1006/JMBI.1995.0350 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.M.JOUVE,P.GOUET,N.BOUDJADA,G.BUISSON,R.KAHN,E.DUEE REMARK 1 TITL CRYSTALLIZATION AND CRYSTAL PACKING OF PROTEUS MIRABILIS PR REMARK 1 TITL 2 CATALASE REMARK 1 REF J.MOL.BIOL. V. 221 1075 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 1942042 REMARK 1 DOI 10.1016/0022-2836(91)90918-V REMARK 1 REFERENCE 4 REMARK 1 AUTH I.FITA,A.M.SILVA,M.R.N.MURTHY,M.G.ROSSMANN REMARK 1 TITL THE REFINED STRUCTURE OF BEEF LIVER CATALASE AT 2.5 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.B V. 42 497 1986 REMARK 1 REFN ISSN 0108-7681 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2727867.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35932 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) : 0.237 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1794 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8676 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 464 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3863 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.33000 REMARK 3 B22 (A**2) : 10.33000 REMARK 3 B33 (A**2) : -20.65000 REMARK 3 B12 (A**2) : 1.89000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.39 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.360 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) : 0.818 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.135 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.325 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.651 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 40.76 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : HEM.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : HEM.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMINO ACIDS 358 - 362 ARE NOT REFINED REMARK 4 REMARK 4 1H7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1290008287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9574 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 : 35932 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 15.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 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 <I/SIGMA(I)> FOR SHELL : NULL 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: PDB ENTRY 1CAE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP AT 4 DEG C, PH 7.30, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 167.46667 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 83.73333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 167.46667 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 83.73333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 167.46667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 83.73333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 167.46667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 83.73333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 46220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -288.6 KCAL/MOL 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 -1.000000 0.000000 0.000000 110.00000 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 350 BIOMT1 3 -1.000000 0.000000 0.000000 110.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2022 LIES ON A SPECIAL POSITION. 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 GLU A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 480 REMARK 465 LYS A 481 REMARK 465 ASP A 482 REMARK 465 ALA A 483 REMARK 465 LYS A 484 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 479 CA C O CB CG CD OE1 REMARK 470 GLU A 479 OE2 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASN A 18 C ASN A 18 O 0.154 REMARK 500 ASN A 18 C ASN A 19 N -0.208 REMARK 500 ARG A 99 NE ARG A 99 CZ 0.227 REMARK 500 ARG A 99 CZ ARG A 99 NH1 -0.186 REMARK 500 THR A 153 CA THR A 153 CB -0.189 REMARK 500 HIS A 349 CG HIS A 349 CD2 -0.158 REMARK 500 ALA A 356 C PRO A 357 N -0.145 REMARK 500 PRO A 357 N PRO A 357 CA 0.191 REMARK 500 TYR A 364 CB TYR A 364 CG -0.150 REMARK 500 TYR A 364 C HIS A 365 N 0.192 REMARK 500 GLU A 472 CD GLU A 472 OE2 0.144 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 6 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 ASN A 18 CA - C - O ANGL. DEV. = -14.4 DEGREES REMARK 500 HIS A 54 O - C - N ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG A 99 NH1 - CZ - NH2 ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 99 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -14.2 DEGREES REMARK 500 ASP A 103 CB - CG - OD2 ANGL. DEV. = -10.7 DEGREES REMARK 500 ASN A 317 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 HIS A 349 CB - CG - CD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 HIS A 349 CB - CG - ND1 ANGL. DEV. = -11.8 DEGREES REMARK 500 PRO A 357 CA - N - CD ANGL. DEV. = -11.5 DEGREES REMARK 500 TYR A 364 CB - CG - CD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 TYR A 364 CB - CG - CD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 HIS A 365 N - CA - CB ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 413 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 101 -176.17 -64.42 REMARK 500 LYS A 148 -156.77 -98.89 REMARK 500 SER A 196 -63.98 65.54 REMARK 500 TYR A 199 -168.23 -110.27 REMARK 500 PRO A 275 3.12 -69.15 REMARK 500 ASN A 348 36.50 -95.17 REMARK 500 ASP A 367 -137.07 55.44 REMARK 500 ASN A 375 -175.68 76.24 REMARK 500 LEU A 478 -90.58 -86.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 103 0.09 SIDE CHAIN REMARK 500 HIS A 349 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 18 12.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 600 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 337 OH REMARK 620 2 HEM A 600 NA 92.7 REMARK 620 3 HEM A 600 NB 90.8 90.5 REMARK 620 4 HEM A 600 NC 90.1 177.3 89.8 REMARK 620 5 HEM A 600 ND 90.9 89.9 178.2 89.7 REMARK 620 N 1 2 3 4 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 600 REMARK 999 REMARK 999 SEQUENCE REMARK 999 MODRES: 1H7K OMT A 53() METHIONINE SULFONE REMARK 999 (S-DIOXYMETHIONINE) REMARK 999 MODRES: 1H7K TYR A 337() OXYGEN OF THE PROXIMAL TYROSINE REMARK 999 337 IS DEPROTONATED DBREF 1H7K A 2 484 UNP P42321 CATA_PROMI 2 484 SEQADV 1H7K TYR A 215 UNP P42321 PHE 215 CONFLICT SEQADV 1H7K OMT A 53 UNP P42321 MET 53 MODIFIED RESIDUE SEQRES 1 A 483 GLU LYS LYS LYS LEU THR THR ALA ALA GLY ALA PRO VAL SEQRES 2 A 483 VAL ASP ASN ASN ASN VAL ILE THR ALA GLY PRO ARG GLY SEQRES 3 A 483 PRO MET LEU LEU GLN ASP VAL TRP PHE LEU GLU LYS LEU SEQRES 4 A 483 ALA HIS PHE ASP ARG GLU VAL ILE PRO GLU ARG ARG OMT SEQRES 5 A 483 HIS ALA LYS GLY SER GLY ALA PHE GLY THR PHE THR VAL SEQRES 6 A 483 THR HIS ASP ILE THR LYS TYR THR ARG ALA LYS ILE PHE SEQRES 7 A 483 SER GLU VAL GLY LYS LYS THR GLU MET PHE ALA ARG PHE SEQRES 8 A 483 SER THR VAL ALA GLY GLU ARG GLY ALA ALA ASP ALA GLU SEQRES 9 A 483 ARG ASP ILE ARG GLY PHE ALA LEU LYS PHE TYR THR GLU SEQRES 10 A 483 GLU GLY ASN TRP ASP MET VAL GLY ASN ASN THR PRO VAL SEQRES 11 A 483 PHE TYR LEU ARG ASP PRO LEU LYS PHE PRO ASP LEU ASN SEQRES 12 A 483 HIS ILE VAL LYS ARG ASP PRO ARG THR ASN MET ARG ASN SEQRES 13 A 483 MET ALA TYR LYS TRP ASP PHE PHE SER HIS LEU PRO GLU SEQRES 14 A 483 SER LEU HIS GLN LEU THR ILE ASP MET SER ASP ARG GLY SEQRES 15 A 483 LEU PRO LEU SER TYR ARG PHE VAL HIS GLY PHE GLY SER SEQRES 16 A 483 HIS THR TYR SER PHE ILE ASN LYS ASP ASN GLU ARG PHE SEQRES 17 A 483 TRP VAL LYS PHE HIS TYR ARG CYS GLN GLN GLY ILE LYS SEQRES 18 A 483 ASN LEU MET ASP ASP GLU ALA GLU ALA LEU VAL GLY LYS SEQRES 19 A 483 ASP ARG GLU SER SER GLN ARG ASP LEU PHE GLU ALA ILE SEQRES 20 A 483 GLU ARG GLY ASP TYR PRO ARG TRP LYS LEU GLN ILE GLN SEQRES 21 A 483 ILE MET PRO GLU LYS GLU ALA SER THR VAL PRO TYR ASN SEQRES 22 A 483 PRO PHE ASP LEU THR LYS VAL TRP PRO HIS ALA ASP TYR SEQRES 23 A 483 PRO LEU MET ASP VAL GLY TYR PHE GLU LEU ASN ARG ASN SEQRES 24 A 483 PRO ASP ASN TYR PHE SER ASP VAL GLU GLN ALA ALA PHE SEQRES 25 A 483 SER PRO ALA ASN ILE VAL PRO GLY ILE SER PHE SER PRO SEQRES 26 A 483 ASP LYS MET LEU GLN GLY ARG LEU PHE SER TYR GLY ASP SEQRES 27 A 483 ALA HIS ARG TYR ARG LEU GLY VAL ASN HIS HIS GLN ILE SEQRES 28 A 483 PRO VAL ASN ALA PRO LYS CYS PRO PHE HIS ASN TYR HIS SEQRES 29 A 483 ARG ASP GLY ALA MET ARG VAL ASP GLY ASN SER GLY ASN SEQRES 30 A 483 GLY ILE THR TYR GLU PRO ASN SER GLY GLY VAL PHE GLN SEQRES 31 A 483 GLU GLN PRO ASP PHE LYS GLU PRO PRO LEU SER ILE GLU SEQRES 32 A 483 GLY ALA ALA ASP HIS TRP ASN HIS ARG GLU ASP GLU ASP SEQRES 33 A 483 TYR PHE SER GLN PRO ARG ALA LEU TYR GLU LEU LEU SER SEQRES 34 A 483 ASP ASP GLU HIS GLN ARG MET PHE ALA ARG ILE ALA GLY SEQRES 35 A 483 GLU LEU SER GLN ALA SER LYS GLU THR GLN GLN ARG GLN SEQRES 36 A 483 ILE ASP LEU PHE THR LYS VAL HIS PRO GLU TYR GLY ALA SEQRES 37 A 483 GLY VAL GLU LYS ALA ILE LYS VAL LEU GLU GLY LYS ASP SEQRES 38 A 483 ALA LYS MODRES 1H7K OMT A 53 MET S-DIOXYMETHIONINE HET OMT A 53 10 HET HEM A 600 43 HET ACT A 700 4 HET SO4 A 800 5 HETNAM OMT S-DIOXYMETHIONINE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM ACT ACETATE ION HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 1 OMT C5 H11 N O4 S FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *168(H2 O) HELIX 1 1 ASP A 33 ASP A 44 1 12 HELIX 2 2 ALA A 76 SER A 80 5 5 HELIX 3 3 ASP A 136 LEU A 138 5 3 HELIX 4 4 LYS A 139 LYS A 148 1 10 HELIX 5 5 ASN A 157 HIS A 167 1 11 HELIX 6 6 LEU A 168 GLU A 170 5 3 HELIX 7 7 SER A 171 SER A 180 1 10 HELIX 8 8 ASP A 181 LEU A 184 5 4 HELIX 9 9 SER A 187 VAL A 191 5 5 HELIX 10 10 MET A 225 ASP A 236 1 12 HELIX 11 11 GLU A 238 ARG A 250 1 13 HELIX 12 12 LYS A 266 THR A 270 5 5 HELIX 13 13 ASN A 303 VAL A 308 1 6 HELIX 14 14 ASP A 327 GLY A 346 1 20 HELIX 15 15 ASN A 348 ILE A 352 5 5 HELIX 16 16 ILE A 352 ALA A 356 5 5 HELIX 17 17 GLN A 393 LYS A 397 5 5 HELIX 18 18 ASN A 411 ASP A 415 5 5 HELIX 19 19 PHE A 419 GLU A 427 1 9 HELIX 20 20 SER A 430 SER A 446 1 17 HELIX 21 21 SER A 449 HIS A 464 1 16 HELIX 22 22 HIS A 464 LEU A 478 1 15 SHEET 1 AA 9 GLY A 57 VAL A 66 0 SHEET 2 AA 9 LYS A 85 THR A 94 -1 O THR A 86 N PHE A 64 SHEET 3 AA 9 ARG A 109 THR A 117 -1 O GLY A 110 N SER A 93 SHEET 4 AA 9 GLY A 120 ASN A 127 -1 O GLY A 120 N THR A 117 SHEET 5 AA 9 GLY A 193 PHE A 194 -1 O PHE A 194 N ASN A 127 SHEET 6 AA 9 ARG A 208 CYS A 217 -1 O TYR A 215 N GLY A 193 SHEET 7 AA 9 ARG A 255 PRO A 264 -1 O LYS A 257 N ARG A 216 SHEET 8 AA 9 MET A 290 ARG A 299 -1 O MET A 290 N ILE A 260 SHEET 9 AA 9 GLY A 57 VAL A 66 -1 O SER A 58 N PHE A 92 LINK C ARG A 52 N OMT A 53 1555 1555 1.33 LINK C OMT A 53 N HIS A 54 1555 1555 1.33 LINK OH TYR A 337 FE HEM A 600 1555 1555 2.10 CISPEP 1 GLU A 383 PRO A 384 0 0.26 SITE 1 AC1 4 GLU A 38 HIS A 42 ARG A 342 HIS A 349 SITE 1 AC2 2 ARG A 423 HOH A2159 SITE 1 AC3 22 ASP A 44 ARG A 51 HIS A 54 ARG A 91 SITE 2 AC3 22 GLY A 110 VAL A 125 GLY A 126 ASN A 127 SITE 3 AC3 22 PRO A 137 PHE A 140 SER A 196 HIS A 197 SITE 4 AC3 22 PHE A 313 MET A 329 ARG A 333 SER A 336 SITE 5 AC3 22 TYR A 337 HIS A 341 ARG A 344 HOH A2038 SITE 6 AC3 22 HOH A2167 HOH A2168 CRYST1 110.000 110.000 251.200 90.00 90.00 120.00 P 62 2 2 12 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 0.009091 0.005249 0.000000 0.00000 SCALE2 0.000000 0.010497 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003981 0.00000