HEADER OXIDOREDUCTASE 13-APR-05 2BOQ TITLE CRYSTAL STRUCTURE OF VERSATILE PEROXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VERSATILE PEROXIDASE VPL2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VERSATILE PEROXIDASE; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE ENZYME OXIDIZES MN(II) AND ALSO COMPND 7 EXHIBITED MN-INDEPENDENT PEROXIDASE ACTIVITY ON DYES AND COMPND 8 PHENOLIC AND NON-PHENOLIC AROMATIC SUBSTRATES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS ERYNGII; SOURCE 3 ORGANISM_COMMON: THISTLE MUSHROOM; SOURCE 4 ORGANISM_TAXID: 5323; SOURCE 5 STRAIN: IJFM A169; SOURCE 6 VARIANT: VPL2; SOURCE 7 ORGAN: HETEROKARYOTIC MYCELLIUM; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: W3110; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PFLAG1-VPL2 KEYWDS OXIDOREDUCTASE, ALLELIC VARIANT, AROMATIC-SUBSTRATE KEYWDS 2 BINDING, CLASS II (FUNGAL) PEROXIDASES, ELECTRON TRANSFER, KEYWDS 3 HOMOLOGY MODELING, LIGNIN PEROXIDASE, LIGNIN DEGRADATION, KEYWDS 4 MANGANESE PEROXIDASE, MN-INDEPENDENT OXIDATION PHENOLIC KEYWDS 5 NON-PHENOLIC AROMATICS, MNII OXIDATION, PEROXIDASE, KEYWDS 6 POLYVALENT PEROXIDASE EXPDTA X-RAY DIFFRACTION AUTHOR T.CHOINOWSKI,K.PIONTEK,A.T.MARTINEZ,M.PEREZ-BOADA REVDAT 3 24-FEB-09 2BOQ 1 VERSN REVDAT 2 14-NOV-05 2BOQ 1 JRNL REVDAT 1 02-NOV-05 2BOQ 0 JRNL AUTH M.PEREZ-BOADA,F.J.RUIZ-DUENAS,R.POGNI,R.BASOSI, JRNL AUTH 2 T.CHOINOWSKI,M.J.MARTINEZ,K.PIONTEK,A.T.MARTINEZ JRNL TITL VERSATILE PEROXIDASE OXIDATION OF HIGH REDOX JRNL TITL 2 POTENTIAL AROMATIC COMPOUNDS: SITE-DIRECTED JRNL TITL 3 MUTAGENESIS, SPECTROSCOPIC AND CRYSTALLOGRAPHIC JRNL TITL 4 INVESTIGATION OF THREE LONG-RANGE ELECTRON JRNL TITL 5 TRANSFER PATHWAYS. JRNL REF J.MOL.BIOL. V. 354 385 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16246366 JRNL DOI 10.1016/J.JMB.2005.09.047 REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 81833 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4321 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) : 1.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5925 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 292 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2404 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 384 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.23000 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): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.835 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2524 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3468 ; 1.796 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 5.752 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1995 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1323 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 294 ; 0.233 ; 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): 44 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.268 ; 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): 1624 ; 1.065 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2619 ; 1.859 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 900 ; 2.794 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 849 ; 4.146 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. RESIDUES 320 - 331 ARE DISORDERED THE REMARK 3 PROTEIN WAS TREATED WITH 6 EQUIVALENTS HYDROGEN PEROXIDE PRIOR REMARK 3 TO CRYSTALLIZATION REMARK 4 REMARK 4 2BOQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-05. REMARK 100 THE PDBE ID CODE IS EBI-23630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91839 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86158 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 80.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: FOR SEARCH MODEL NO WWPDB ENTRY AVAILABLE YET REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.6 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYST9 MG/ML PROTEIN, 10 MM REMARK 280 SODIUM TARTRATE PH=5.5 17% PEG10000, 200MM ZN ACETATE, REMARK 280 100 MM SODIUM CACODYLATE PH=6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.11100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.66650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.55550 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 320 REMARK 465 PRO A 321 REMARK 465 VAL A 322 REMARK 465 THR A 323 REMARK 465 SER A 324 REMARK 465 VAL A 325 REMARK 465 PRO A 326 REMARK 465 PRO A 327 REMARK 465 VAL A 328 REMARK 465 PRO A 329 REMARK 465 GLY A 330 REMARK 465 SER A 331 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 OE1 GLU A 40 - O HOH A 2064 2.05 REMARK 500 OD1 ASP A 69 - O HOH A 2105 2.15 REMARK 500 OD2 ASP A 128 - O HOH A 2177 2.19 REMARK 500 OD2 ASP A 146 - O HOH A 2209 2.13 REMARK 500 OD2 ASP A 175 - O HOH A 2230 2.02 REMARK 500 O HOH A 2027 - O HOH A 2086 2.13 REMARK 500 O HOH A 2127 - O HOH A 2230 2.05 REMARK 500 O HOH A 2187 - O HOH A 2194 2.16 REMARK 500 O HOH A 2310 - O HOH A 2315 2.02 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 REMARK 500 O HOH A 2134 O HOH A 2262 3654 2.07 REMARK 500 O HOH A 2240 O HOH A 2357 3654 1.87 REMARK 500 O HOH A 2316 O HOH A 2331 4575 2.10 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 4 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 318 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 289 22.1 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): 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 ZN A1323 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 30 OD2 REMARK 620 2 GLU A 37 OE1 83.5 REMARK 620 3 GLU A 37 OE2 122.3 50.3 REMARK 620 4 HIS A 232 NE2 120.3 154.5 105.2 REMARK 620 5 HOH A2376 O 102.4 86.0 105.8 96.4 REMARK 620 6 ASP A 30 OD1 52.2 91.1 91.3 97.0 154.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1324 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 26 OE1 REMARK 620 2 HOH A2377 O 93.9 REMARK 620 3 ASP A 237 OD1 153.5 84.0 REMARK 620 4 ASP A 237 OD2 104.6 107.5 51.8 REMARK 620 5 HOH A2378 O 122.4 111.6 82.4 114.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1325 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 136 ND1 REMARK 620 2 CAC A1329 O1 119.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1327 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 140 OE1 REMARK 620 2 ASP A 143 OD1 117.5 REMARK 620 3 CAC A1329 O2 122.4 108.8 REMARK 620 4 ASP A 143 OD2 103.5 51.6 79.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1358 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2380 O REMARK 620 2 HOH A2379 O 89.9 REMARK 620 3 HIS A 293 NE2 95.4 91.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1359 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 HOH A2381 O 114.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1360 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2384 O REMARK 620 2 HOH A2177 O 167.2 REMARK 620 3 HOH A2383 O 92.2 83.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1328 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 36 OE2 REMARK 620 2 HEM A1320 O1D 117.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CAC A1329 AS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CAC A1329 O2 REMARK 620 2 CAC A1329 O1 110.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1351 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 62 OD1 REMARK 620 2 SER A 64 OG 76.3 REMARK 620 3 ASP A 48 O 137.0 144.5 REMARK 620 4 ASP A 48 OD1 84.1 91.3 82.6 REMARK 620 5 GLY A 60 O 70.3 145.2 70.3 94.8 REMARK 620 6 HOH A2081 O 99.2 80.0 101.1 169.6 95.6 REMARK 620 7 HOH A2110 O 148.7 73.4 71.6 89.2 140.9 82.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1352 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 170 O REMARK 620 2 THR A 189 O 82.4 REMARK 620 3 SER A 170 OG 72.9 147.2 REMARK 620 4 ASP A 187 OD1 79.0 76.1 118.5 REMARK 620 5 ASP A 187 OD2 90.9 125.7 76.8 49.8 REMARK 620 6 THR A 189 OG1 147.3 70.1 139.0 77.5 91.1 REMARK 620 7 VAL A 192 O 86.9 76.8 80.6 150.8 157.0 103.0 REMARK 620 8 ASP A 194 OD1 141.4 128.5 69.2 125.9 87.4 71.3 80.3 REMARK 620 N 1 2 3 4 5 6 7 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 HEM A1320 NA REMARK 620 2 HEM A1320 ND 89.1 REMARK 620 3 HIS A 169 NE2 100.8 100.9 REMARK 620 4 HEM A1320 NC 159.1 87.2 100.1 REMARK 620 5 HOH A2073 O 78.5 80.3 178.6 80.6 REMARK 620 6 HEM A1320 NB 87.6 160.1 99.0 89.0 79.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1323 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1324 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1325 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1326 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1327 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1328 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A1329 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1358 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1359 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1320 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQADV RECORDS SHOWN BELOW ARISE DUE TO A SPONTANEOUS REMARK 999 MUTATION (GLU 191 GLY) WHEN CLONING THE VERSATILE REMARK 999 VERSATILE PEROXIDASE (VPL2) PRECURSOR CDNA. DBREF 2BOQ A 1 331 UNP O94753 O94753_9AGAR 31 361 SEQADV 2BOQ GLU A 191 UNP O94753 GLY 221 CONFLICT SEE REMARK 999 SEQRES 1 A 331 ALA THR CYS ASP ASP GLY ARG THR THR ALA ASN ALA ALA SEQRES 2 A 331 CYS CYS ILE LEU PHE PRO ILE LEU ASP ASP ILE GLN GLU SEQRES 3 A 331 ASN LEU PHE ASP GLY ALA GLN CYS GLY GLU GLU VAL HIS SEQRES 4 A 331 GLU SER LEU ARG LEU THR PHE HIS ASP ALA ILE GLY PHE SEQRES 5 A 331 SER PRO THR LEU GLY GLY GLY GLY ALA ASP GLY SER ILE SEQRES 6 A 331 ILE ALA PHE ASP THR ILE GLU THR ASN PHE PRO ALA ASN SEQRES 7 A 331 ALA GLY ILE ASP GLU ILE VAL SER ALA GLN LYS PRO PHE SEQRES 8 A 331 VAL ALA LYS HIS ASN ILE SER ALA GLY ASP PHE ILE GLN SEQRES 9 A 331 PHE ALA GLY ALA VAL GLY VAL SER ASN CYS PRO GLY GLY SEQRES 10 A 331 VAL ARG ILE PRO PHE PHE LEU GLY ARG PRO ASP ALA VAL SEQRES 11 A 331 ALA ALA SER PRO ASP HIS LEU VAL PRO GLU PRO PHE ASP SEQRES 12 A 331 SER VAL ASP SER ILE LEU ALA ARG MET GLY ASP ALA GLY SEQRES 13 A 331 PHE SER PRO VAL GLU VAL VAL TRP LEU LEU ALA SER HIS SEQRES 14 A 331 SER ILE ALA ALA ALA ASP LYS VAL ASP PRO SER ILE PRO SEQRES 15 A 331 GLY THR PRO PHE ASP SER THR PRO GLU VAL PHE ASP SER SEQRES 16 A 331 GLN PHE PHE ILE GLU THR GLN LEU LYS GLY ARG LEU PHE SEQRES 17 A 331 PRO GLY THR ALA ASP ASN LYS GLY GLU ALA GLN SER PRO SEQRES 18 A 331 LEU GLN GLY GLU ILE ARG LEU GLN SER ASP HIS LEU LEU SEQRES 19 A 331 ALA ARG ASP PRO GLN THR ALA CYS GLU TRP GLN SER MET SEQRES 20 A 331 VAL ASN ASN GLN PRO LYS ILE GLN ASN ARG PHE ALA ALA SEQRES 21 A 331 THR MET SER LYS MET ALA LEU LEU GLY GLN ASP LYS THR SEQRES 22 A 331 LYS LEU ILE ASP CYS SER ASP VAL ILE PRO THR PRO PRO SEQRES 23 A 331 ALA LEU VAL GLY ALA ALA HIS LEU PRO ALA GLY PHE SER SEQRES 24 A 331 LEU SER ASP VAL GLU GLN ALA CYS ALA ALA THR PRO PHE SEQRES 25 A 331 PRO ALA LEU THR ALA ASP PRO GLY PRO VAL THR SER VAL SEQRES 26 A 331 PRO PRO VAL PRO GLY SER HET ZN A1323 1 HET ZN A1324 1 HET ZN A1325 1 HET ZN A1326 1 HET ZN A1327 1 HET MN A1328 1 HET CAC A1329 5 HET CA A1351 1 HET CA A1352 1 HET ZN A1358 1 HET ZN A1359 1 HET ZN A1360 1 HET HEM A1320 43 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM CAC CACODYLATE ION HETNAM CA CALCIUM ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM [DIHYDROGEN 3,7,12,17-TETRAMETHYL-8,13- HETSYN 2 HEM DIVINYL-2,18-PORPHINEDIPROPIONATO(2-)]IRON FORMUL 2 ZN 8(ZN 2+) FORMUL 7 MN MN 2+ FORMUL 8 CAC C2 H6 AS O2 1- FORMUL 9 CA 2(CA 2+) FORMUL 14 HEM C34 H32 FE N4 O4 FORMUL 15 HOH *384(H2 O1) 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 ALA A 155 1 12 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 MET 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 2.06 SSBOND 3 CYS A 34 CYS A 114 1555 1555 2.06 SSBOND 4 CYS A 242 CYS A 307 1555 1555 2.13 LINK FE HEM A1320 NE2 HIS A 169 1555 1555 2.13 LINK FE HEM A1320 O HOH A2073 1555 1555 2.70 LINK ZN ZN A1323 OE2 GLU A 37 1555 1555 1.93 LINK ZN ZN A1323 NE2 HIS A 232 1555 3654 2.01 LINK ZN ZN A1323 O HOH A2376 1555 1555 1.98 LINK ZN ZN A1323 OD1 ASP A 30 1555 1555 2.67 LINK ZN ZN A1323 OE1 GLU A 37 1555 1555 2.77 LINK ZN ZN A1323 OD2 ASP A 30 1555 1555 1.92 LINK ZN ZN A1324 OD1 ASP A 237 1555 1555 2.75 LINK ZN ZN A1324 OD2 ASP A 237 1555 1555 1.96 LINK ZN ZN A1324 O HOH A2378 1555 1555 2.13 LINK ZN ZN A1324 OE1 GLU A 26 1555 4565 1.87 LINK ZN ZN A1324 O HOH A2377 1555 1555 1.98 LINK ZN ZN A1325 ND1 HIS A 136 1555 1555 2.08 LINK ZN ZN A1325 O1 CAC A1329 1555 1555 1.86 LINK ZN ZN A1327 OD2 ASP A 143 1555 1555 2.73 LINK ZN ZN A1327 OE1 GLU A 140 1555 1555 1.86 LINK ZN ZN A1327 O2 CAC A1329 1555 1555 1.91 LINK ZN ZN A1327 OD1 ASP A 143 1555 1555 1.95 LINK MN MN A1328 O1D HEM A1320 1555 1555 2.08 LINK MN MN A1328 OE2 GLU A 36 1555 1555 1.82 LINK CA CA A1351 OG SER A 64 1555 1555 2.40 LINK CA CA A1351 O ASP A 48 1555 1555 2.44 LINK CA CA A1351 OD1 ASP A 48 1555 1555 2.32 LINK CA CA A1351 O GLY A 60 1555 1555 2.46 LINK CA CA A1351 O HOH A2081 1555 1555 2.34 LINK CA CA A1351 OD1 ASP A 62 1555 1555 2.42 LINK CA CA A1351 O HOH A2110 1555 1555 2.49 LINK CA CA A1352 OD1 ASP A 194 1555 1555 2.47 LINK CA CA A1352 OG1 THR A 189 1555 1555 2.51 LINK CA CA A1352 O VAL A 192 1555 1555 2.40 LINK CA CA A1352 OG SER A 170 1555 1555 2.52 LINK CA CA A1352 OD1 ASP A 187 1555 1555 2.70 LINK CA CA A1352 O SER A 170 1555 1555 2.35 LINK CA CA A1352 O THR A 189 1555 1555 2.40 LINK CA CA A1352 OD2 ASP A 187 1555 1555 2.39 LINK ZN ZN A1358 NE2 HIS A 293 1555 1555 2.17 LINK ZN ZN A1358 O HOH A2379 1555 1555 1.88 LINK ZN ZN A1358 O HOH A2380 1555 1555 2.07 LINK ZN ZN A1359 O HOH A2381 1555 1555 1.98 LINK ZN ZN A1359 ND1 HIS A 95 1555 1555 2.28 LINK ZN ZN A1360 O HOH A2383 1555 1555 2.11 LINK ZN ZN A1360 O HOH A2177 1555 1555 2.29 LINK ZN ZN A1360 O HOH A2384 1555 1555 1.92 CISPEP 1 VAL A 289 GLY A 290 0 -24.29 SITE 1 AC1 5 ASP A 30 GLU A 37 HIS A 232 ARG A 236 SITE 2 AC1 5 HOH A2376 SITE 1 AC2 4 GLU A 26 ASP A 237 HOH A2377 HOH A2378 SITE 1 AC3 4 HIS A 136 GLU A 140 ZN A1326 CAC A1329 SITE 1 AC4 3 GLU A 140 ZN A1325 ZN A1327 SITE 1 AC5 4 GLU A 140 ASP A 143 ZN A1326 CAC A1329 SITE 1 AC6 3 GLU A 36 ASP A 175 HEM A1320 SITE 1 AC7 7 HIS A 136 VAL A 138 GLU A 140 ASP A 143 SITE 2 AC7 7 ZN A1325 ZN A1327 HOH A2195 SITE 1 AC8 6 ASP A 48 GLY A 60 ASP A 62 SER A 64 SITE 2 AC8 6 HOH A2081 HOH A2110 SITE 1 AC9 5 SER A 170 ASP A 187 THR A 189 VAL A 192 SITE 2 AC9 5 ASP A 194 SITE 1 BC1 4 HIS A 293 ASP A 318 HOH A2379 HOH A2380 SITE 1 BC2 3 HIS A 95 HOH A2024 HOH A2381 SITE 1 BC3 4 HOH A2177 HOH A2382 HOH A2383 HOH A2384 SITE 1 BC4 27 GLU A 36 HIS A 39 GLU A 40 LEU A 42 SITE 2 BC4 27 ARG A 43 PHE A 46 PRO A 139 GLU A 140 SITE 3 BC4 27 PRO A 141 LEU A 165 LEU A 166 SER A 168 SITE 4 BC4 27 HIS A 169 ALA A 172 ALA A 173 ALA A 174 SITE 5 BC4 27 ASP A 175 LYS A 176 VAL A 177 PHE A 186 SITE 6 BC4 27 LEU A 228 SER A 230 MN A1328 HOH A2060 SITE 7 BC4 27 HOH A2073 HOH A2374 HOH A2375 CRYST1 62.799 62.799 98.222 90.00 90.00 90.00 P 43 4 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 0.015924 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010181 0.00000