HEADER OXIDOREDUCTASE 18-DEC-07 2VKA TITLE SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN TITLE 2 PLEUROTUS ERYNGII VERSATILE PEROXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VERSATILE PEROXIDASE VPL2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 31-347; COMPND 5 SYNONYM: VERSATILE LIQUID PHASE PEROXIDASE 2; COMPND 6 EC: 1.11.1.16; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS ERYNGII; SOURCE 3 ORGANISM_COMMON: THISTLE MUSHROOM; SOURCE 4 ORGANISM_TAXID: 5323; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGNIN PEROXIDASE, LIGNIN DEGRADATION, MANGANESE PEROXIDASE, KEYWDS 2 POLYVALENT PEROXIDASE, AROMATIC-SUBSTRATE BINDING, MN-INDEPENDENT KEYWDS 3 OXIDATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.J.RUIZ-DUENAS,M.MORALES,M.J.MATE,A.ROMERO,M.J.MARTINEZ,A.SMITH, AUTHOR 2 A.T.MARTINEZ REVDAT 5 16-OCT-24 2VKA 1 REMARK REVDAT 4 13-DEC-23 2VKA 1 LINK REVDAT 3 13-JUL-11 2VKA 1 VERSN REVDAT 2 24-FEB-09 2VKA 1 VERSN REVDAT 1 29-JAN-08 2VKA 0 JRNL AUTH F.J.RUIZ-DUENAS,M.MORALES,M.J.MATE,A.ROMERO,M.J.MARTINEZ, JRNL AUTH 2 A.SMITH,A.T.MARTINEZ JRNL TITL SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN JRNL TITL 2 ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE JRNL REF BIOCHEMISTRY V. 47 1685 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18201105 JRNL DOI 10.1021/BI7020298 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0036 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 30108 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1484 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 8.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 26.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 374 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE SET COUNT : 21 REMARK 3 BIN FREE R VALUE : 0.1870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2344 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 418 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : UNVERIFIED REMARK 3 FROM WILSON PLOT (A**2) : 14.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34100 REMARK 3 B22 (A**2) : -0.34100 REMARK 3 B33 (A**2) : 0.68300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.948 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2484 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3407 ; 1.515 ; 2.014 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 6.338 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;37.024 ;25.143 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 352 ;12.152 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;21.368 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1946 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1337 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1735 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 345 ; 0.190 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 33 ; 0.215 ; 0.200 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): 1640 ; 0.737 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2566 ; 1.134 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 940 ; 1.917 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 839 ; 2.873 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 400 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9644 16.0208 -0.0130 REMARK 3 T TENSOR REMARK 3 T11: -0.1189 T22: -0.1144 REMARK 3 T33: -0.0993 T12: 0.0042 REMARK 3 T13: 0.0153 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.6789 L22: 1.1514 REMARK 3 L33: 0.9685 L12: 0.1425 REMARK 3 L13: 0.1650 L23: 0.3580 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: -0.0356 S13: -0.0115 REMARK 3 S21: 0.0351 S22: -0.0017 S23: -0.0235 REMARK 3 S31: 0.0164 S32: 0.0264 S33: 0.0192 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9330 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30110 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.150 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7200 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) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.18 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BOQ REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE AND 100 MM REMARK 280 SODIUM CACODILATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 48.14500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 48.14500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.26500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.63250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.14500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.89750 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.14500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.14500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.26500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 48.14500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 73.89750 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 48.14500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.63250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 A2020 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2051 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2099 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2266 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, MET 277 TO PHE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2067 O HOH A 2190 2.04 REMARK 500 O HOH A 2408 O HOH A 2410 2.05 REMARK 500 OE1 GLU A 36 O HOH A 2058 2.10 REMARK 500 O HOH A 2372 O HOH A 2373 2.13 REMARK 500 O HOH A 2288 O HOH A 2289 2.15 REMARK 500 O HOH A 2056 O HOH A 2101 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2224 O HOH A 2389 3555 2.11 REMARK 500 O HOH A 2218 O HOH A 2387 3555 2.15 REMARK 500 O HOH A 2036 O HOH A 2036 6555 2.15 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 ASP A 187 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 206 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 206 NE - CZ - NH2 ANGL. DEV. = 7.4 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 ASN A 250 58.93 -140.82 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 CA A1321 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 48 OD1 REMARK 620 2 ASP A 48 O 82.4 REMARK 620 3 GLY A 60 O 96.0 71.7 REMARK 620 4 ASP A 62 OD1 85.5 139.5 71.3 REMARK 620 5 SER A 64 OG 90.4 139.7 148.6 78.7 REMARK 620 6 HOH A2074 O 167.3 101.2 96.7 99.0 79.0 REMARK 620 7 HOH A2103 O 88.8 66.9 137.2 151.4 73.4 81.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1320 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 169 NE2 REMARK 620 2 HEM A1320 NA 99.7 REMARK 620 3 HEM A1320 NB 96.7 89.9 REMARK 620 4 HEM A1320 NC 95.9 164.3 89.5 REMARK 620 5 HEM A1320 ND 98.7 86.4 164.6 90.1 REMARK 620 6 HOH A2071 O 177.3 77.7 82.4 86.6 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1319 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 170 O REMARK 620 2 SER A 170 OG 74.0 REMARK 620 3 ASP A 187 OD1 76.5 115.2 REMARK 620 4 ASP A 187 OD2 92.6 75.7 49.6 REMARK 620 5 THR A 189 OG1 146.1 139.3 81.0 91.7 REMARK 620 6 THR A 189 O 82.0 149.3 76.2 125.0 68.2 REMARK 620 7 VAL A 192 O 86.6 83.5 149.3 158.5 100.8 76.2 REMARK 620 8 ASP A 194 OD1 142.0 68.9 127.2 86.3 71.8 128.7 81.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1320 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1321 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1322 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BOQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VERSATILE PEROXIDASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATION M247F DBREF 2VKA A 1 317 UNP O94753 O94753_PLEER 31 347 SEQADV 2VKA PHE A 247 UNP O94753 MET 277 ENGINEERED MUTATION SEQRES 1 A 317 ALA THR CYS ASP ASP GLY ARG THR THR ALA ASN ALA ALA SEQRES 2 A 317 CYS CYS ILE LEU PHE PRO ILE LEU ASP ASP ILE GLN GLU SEQRES 3 A 317 ASN LEU PHE ASP GLY ALA GLN CYS GLY GLU GLU VAL HIS SEQRES 4 A 317 GLU SER LEU ARG LEU THR PHE HIS ASP ALA ILE GLY PHE SEQRES 5 A 317 SER PRO THR LEU GLY GLY GLY GLY ALA ASP GLY SER ILE SEQRES 6 A 317 ILE ALA PHE ASP THR ILE GLU THR ASN PHE PRO ALA ASN SEQRES 7 A 317 ALA GLY ILE ASP GLU ILE VAL SER ALA GLN LYS PRO PHE SEQRES 8 A 317 VAL ALA LYS HIS ASN ILE SER ALA GLY ASP PHE ILE GLN SEQRES 9 A 317 PHE ALA GLY ALA VAL GLY VAL SER ASN CYS PRO GLY GLY SEQRES 10 A 317 VAL ARG ILE PRO PHE PHE LEU GLY ARG PRO ASP ALA VAL SEQRES 11 A 317 ALA ALA SER PRO ASP HIS LEU VAL PRO GLU PRO PHE ASP SEQRES 12 A 317 SER VAL ASP SER ILE LEU ALA ARG MET GLY ASP ALA GLY SEQRES 13 A 317 PHE SER PRO VAL GLU VAL VAL TRP LEU LEU ALA SER HIS SEQRES 14 A 317 SER ILE ALA ALA ALA ASP LYS VAL ASP PRO SER ILE PRO SEQRES 15 A 317 GLY THR PRO PHE ASP SER THR PRO GLY VAL PHE ASP SER SEQRES 16 A 317 GLN PHE PHE ILE GLU THR GLN LEU LYS GLY ARG LEU PHE SEQRES 17 A 317 PRO GLY THR ALA ASP ASN LYS GLY GLU ALA GLN SER PRO SEQRES 18 A 317 LEU GLN GLY GLU ILE ARG LEU GLN SER ASP HIS LEU LEU SEQRES 19 A 317 ALA ARG ASP PRO GLN THR ALA CYS GLU TRP GLN SER PHE SEQRES 20 A 317 VAL ASN ASN GLN PRO LYS ILE GLN ASN ARG PHE ALA ALA SEQRES 21 A 317 THR MET SER LYS MET ALA LEU LEU GLY GLN ASP LYS THR SEQRES 22 A 317 LYS LEU ILE ASP CYS SER ASP VAL ILE PRO THR PRO PRO SEQRES 23 A 317 ALA LEU VAL GLY ALA ALA HIS LEU PRO ALA GLY PHE SER SEQRES 24 A 317 LEU SER ASP VAL GLU GLN ALA CYS ALA ALA THR PRO PHE SEQRES 25 A 317 PRO ALA LEU THR ALA HET SO4 A1318 5 HET CA A1319 1 HET HEM A1320 43 HET CA A1321 1 HET GOL A1322 6 HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 O4 S 2- FORMUL 3 CA 2(CA 2+) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *418(H2 O) HELIX 1 1 ASN A 11 CYS A 15 5 5 HELIX 2 2 ILE A 16 LEU A 28 1 13 HELIX 3 3 GLY A 35 ILE A 50 1 16 HELIX 4 4 GLY A 63 PHE A 68 1 6 HELIX 5 5 PHE A 68 THR A 73 1 6 HELIX 6 6 ASN A 74 ALA A 79 5 6 HELIX 7 7 ILE A 81 HIS A 95 1 15 HELIX 8 8 SER A 98 ASN A 113 1 16 HELIX 9 9 SER A 144 GLY A 156 1 13 HELIX 10 10 SER A 158 LEU A 166 1 9 HELIX 11 11 ALA A 167 ILE A 171 5 5 HELIX 12 12 SER A 195 THR A 201 1 7 HELIX 13 13 GLN A 229 ALA A 235 1 7 HELIX 14 14 THR A 240 PHE A 247 1 8 HELIX 15 15 ASN A 250 LEU A 267 1 18 HELIX 16 16 ASP A 271 LEU A 275 5 5 HELIX 17 17 SER A 279 ILE A 282 5 4 HELIX 18 18 SER A 299 ASP A 302 5 4 SHEET 1 AA 2 PHE A 123 LEU A 124 0 SHEET 2 AA 2 ILE A 276 ASP A 277 -1 O ILE A 276 N LEU A 124 SHEET 1 AB 2 ALA A 173 ALA A 174 0 SHEET 2 AB 2 THR A 184 PRO A 185 -1 O THR A 184 N ALA A 174 SHEET 1 AC 2 GLU A 217 ALA A 218 0 SHEET 2 AC 2 ARG A 227 LEU A 228 -1 O ARG A 227 N ALA A 218 SSBOND 1 CYS A 3 CYS A 15 1555 1555 2.04 SSBOND 2 CYS A 14 CYS A 278 1555 1555 2.04 SSBOND 3 CYS A 34 CYS A 114 1555 1555 2.05 SSBOND 4 CYS A 242 CYS A 307 1555 1555 2.09 LINK OD1 ASP A 48 CA CA A1321 1555 1555 2.46 LINK O ASP A 48 CA CA A1321 1555 1555 2.53 LINK O GLY A 60 CA CA A1321 1555 1555 2.39 LINK OD1 ASP A 62 CA CA A1321 1555 1555 2.41 LINK OG SER A 64 CA CA A1321 1555 1555 2.56 LINK NE2 HIS A 169 FE HEM A1320 1555 1555 2.16 LINK O SER A 170 CA CA A1319 1555 1555 2.36 LINK OG SER A 170 CA CA A1319 1555 1555 2.56 LINK OD1 ASP A 187 CA CA A1319 1555 1555 2.63 LINK OD2 ASP A 187 CA CA A1319 1555 1555 2.45 LINK OG1 THR A 189 CA CA A1319 1555 1555 2.58 LINK O THR A 189 CA CA A1319 1555 1555 2.40 LINK O VAL A 192 CA CA A1319 1555 1555 2.41 LINK OD1 ASP A 194 CA CA A1319 1555 1555 2.54 LINK FE HEM A1320 O HOH A2071 1555 1555 2.68 LINK CA CA A1321 O HOH A2074 1555 1555 2.38 LINK CA CA A1321 O HOH A2103 1555 1555 2.65 SITE 1 AC1 25 GLU A 36 HIS A 39 GLU A 40 LEU A 42 SITE 2 AC1 25 THR A 45 PHE A 46 GLU A 140 PRO A 141 SITE 3 AC1 25 LEU A 165 LEU A 166 SER A 168 HIS A 169 SITE 4 AC1 25 ALA A 172 ALA A 173 ASP A 175 LYS A 176 SITE 5 AC1 25 VAL A 177 PHE A 186 LEU A 228 SER A 230 SITE 6 AC1 25 HOH A2058 HOH A2071 HOH A2415 HOH A2416 SITE 7 AC1 25 HOH A2417 SITE 1 AC2 9 HIS A 136 GLU A 140 ARG A 206 HOH A2207 SITE 2 AC2 9 HOH A2213 HOH A2411 HOH A2412 HOH A2413 SITE 3 AC2 9 HOH A2414 SITE 1 AC3 5 SER A 170 ASP A 187 THR A 189 VAL A 192 SITE 2 AC3 5 ASP A 194 SITE 1 AC4 6 ASP A 48 GLY A 60 ASP A 62 SER A 64 SITE 2 AC4 6 HOH A2074 HOH A2103 SITE 1 AC5 7 SER A 53 THR A 55 ARG A 151 ASP A 154 SITE 2 AC5 7 GLY A 297 HOH A2231 HOH A2418 CRYST1 96.290 96.290 98.530 90.00 90.00 90.00 I 41 8 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 0.010385 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010149 0.00000