HEADER OXIDOREDUCTASE 16-DEC-08 3FKG TITLE CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM TITLE 2 PLEUROTUS ERYNGII COMPND MOL_ID: 1; COMPND 2 MOLECULE: VERSATILE PEROXIDASE VPL2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VERSATILE LIQUID PHASE PEROXIDASE 2; COMPND 5 EC: 1.11.1.16; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS ERYNGII; SOURCE 3 ORGANISM_COMMON: BOLETUS OF THE STEPPES; SOURCE 4 ORGANISM_TAXID: 5323; SOURCE 5 STRAIN: IJFM, A169; SOURCE 6 GENE: VPL2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: W3110; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFLAG1-VPL2 KEYWDS ALLELIC VARIANT, AROMATIC-SUBSTRATE BINDING, CLASS II (FUNGAL) KEYWDS 2 PEROXIDASES, PROTOPORPHYRIN IX, ELECTRON TRANSFER, LIGNIN KEYWDS 3 PEROXIDASE, LIGNIN DEGRADATION, MANGANESE PEROXIDASE, MN-INDEPENDENT KEYWDS 4 OXIDATION PHENOLIC NON-PHENOLIC AROMATICS, MNII OXIDATION, KEYWDS 5 PEROXIDASE, POLYVALENT PEROXIDASE, OXIDOREDUCTASE, HEME, HYDROGEN KEYWDS 6 PEROXIDE, IRON, MANGANESE, METAL-BINDING, SECRETED, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR K.PIONTEK,A.T.MARTINEZ,T.CHOINOWSKI,D.A.PLATTNER REVDAT 3 01-NOV-23 3FKG 1 REMARK LINK REVDAT 2 13-JUL-11 3FKG 1 VERSN REVDAT 1 22-DEC-09 3FKG 0 JRNL AUTH K.PIONTEK,T.CHOINOWSKI,M.PEREZ-BOADA,F.J.RUIZ-DUENAS, JRNL AUTH 2 M.J.MARTINEZ,D.A.PLATTNER,A.T.MARTINEZ JRNL TITL STRUCTURAL AND SITE-DIRECTED MUTAGENESIS STUDY OF VERSATILE JRNL TITL 2 PEROXIDASE OXIDIZING BOTH MN(II) AND AROMATIC SUBSTRATES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 31531 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1667 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) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2391 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2360 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.07000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.617 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2568 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3503 ; 1.442 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 7.302 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;35.504 ;25.327 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;13.652 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;21.180 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1995 ; 0.017 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1320 ; 0.226 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1798 ; 0.319 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 445 ; 0.210 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.112 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 47 ; 0.258 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.434 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.049 ; 0.200 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): 1674 ; 2.509 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2639 ; 3.344 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 978 ; 3.188 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 855 ; 4.354 ; 3.000 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 : 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3FKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8065 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33318 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39200 REMARK 200 FOR SHELL : 1.100 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: PDB ENTRY 1QPA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9.0MG/ML PROTEIN IN 10MM NA-TARTRATE REMARK 280 PH 5.5, 17% PEG 10000, 200MM ZN-ACETATE, 100MM NA-CACODYLATE PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 49.10850 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 73.66275 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 24.55425 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 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 NE2 HIS A 293 OD2 ASP A 318 2.05 REMARK 500 OE2 GLU A 40 OE1 GLU A 83 2.14 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 96 47.81 -106.04 REMARK 500 ARG A 206 -30.43 -130.16 REMARK 500 LEU A 288 132.62 -39.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 290 ALA A 291 144.74 REMARK 500 ASP A 318 PRO A 319 -147.28 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 ZN A 332 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 30 OD2 REMARK 620 2 GLU A 37 OE2 122.5 REMARK 620 3 GLU A 37 OE1 82.1 53.3 REMARK 620 4 HOH A 404 O 102.4 109.5 88.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 339 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 36 OE1 REMARK 620 2 GLU A 40 OE2 135.6 REMARK 620 3 GLU A 83 OE1 150.3 63.8 REMARK 620 4 GLU A 83 OE2 86.9 100.7 65.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 351 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 48 O REMARK 620 2 ASP A 48 OD1 83.8 REMARK 620 3 GLY A 60 O 71.8 96.5 REMARK 620 4 ASP A 62 OD1 134.8 81.1 68.0 REMARK 620 5 SER A 64 OG 144.9 89.2 143.3 77.2 REMARK 620 6 HOH A 373 O 70.4 88.6 141.0 150.6 75.1 REMARK 620 7 HOH A 441 O 102.9 168.5 94.5 100.0 79.9 85.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 341 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 69 OD1 REMARK 620 2 HOH A 415 O 101.7 REMARK 620 3 HOH A 416 O 103.4 110.6 REMARK 620 4 HOH A 417 O 81.4 159.9 87.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 340 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 83 OE1 REMARK 620 2 ASP A 175 OD2 147.7 REMARK 620 3 HOH A 414 O 108.7 76.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 HOH A 410 O 95.5 REMARK 620 3 HOH A 411 O 114.4 127.1 REMARK 620 4 HOH A 412 O 103.7 114.5 100.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 338 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 136 ND1 REMARK 620 2 CAC A 342 O2 120.3 REMARK 620 3 CAC A 343 O1 118.9 120.2 REMARK 620 4 HOH A 413 O 100.8 91.7 70.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 334 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 140 OE1 REMARK 620 2 ASP A 143 OD1 121.2 REMARK 620 3 CAC A 342 O1 124.2 108.6 REMARK 620 4 CAC A 343 O2 89.6 98.3 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 350 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 169 NE2 REMARK 620 2 HEM A 350 NA 102.4 REMARK 620 3 HEM A 350 NB 100.4 88.3 REMARK 620 4 HEM A 350 NC 99.1 158.5 89.0 REMARK 620 5 HEM A 350 ND 97.8 89.3 161.7 86.6 REMARK 620 6 HOH A 595 O 174.9 78.1 74.5 80.6 87.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 352 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 170 O REMARK 620 2 SER A 170 OG 72.6 REMARK 620 3 ASP A 187 OD1 78.2 118.0 REMARK 620 4 ASP A 187 OD2 92.6 78.5 49.4 REMARK 620 5 THR A 189 O 82.1 147.0 75.5 124.3 REMARK 620 6 THR A 189 OG1 148.5 138.4 79.8 89.9 70.7 REMARK 620 7 VAL A 192 O 87.6 81.3 150.3 158.7 76.8 100.9 REMARK 620 8 ASP A 194 OD1 141.3 69.8 128.5 88.9 127.6 70.1 77.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 337 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 175 OD2 REMARK 620 2 HEM A 350 O1D 113.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 333 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 237 OD2 REMARK 620 2 HOH A 405 O 114.9 REMARK 620 3 HOH A 406 O 109.5 111.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 335 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 408 O REMARK 620 2 HOH A 409 O 70.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 333 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A 343 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BOQ RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE WILD TYPE INCUBATED WITH H2O2 REMARK 900 RELATED ID: 3FJW RELATED DB: PDB REMARK 900 FUNGAL WILD TYPE VERSATILE PEROXIDASE REMARK 900 RELATED ID: 3FM1 RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE G191Q VARIANT, CRYSTALS SOAKED REMARK 900 WITH MN2+ REMARK 900 RELATED ID: 3FM4 RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE D175A VARIANT REMARK 900 RELATED ID: 3FM6 RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE F142Q VARIANT REMARK 900 RELATED ID: 3FMU RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE W164S VARIANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND THE REMARK 999 DATABASE REFERENCE SEQUENCE. THIS CAN BE CALLED AS REMARK 999 SPONTANEITY MUTATION. THE DEPOSITOR PREPARED THE TARGET REMARK 999 PROTEIN AS WILD TYPE, BUT IN THE STRUCTURE TWO (SILENT) REMARK 999 MUTATIONS WERE FOUND. DBREF 3FKG A 1 331 UNP O94753 VPL2_PLEER 31 361 SEQADV 3FKG ASN A 33 UNP O94753 GLN 63 SEE REMARK 999 SEQADV 3FKG GLU A 191 UNP O94753 GLY 221 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 ASN 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 HEM A 350 43 HET CA A 351 1 HET CA A 352 1 HET ZN A 332 1 HET ZN A 333 1 HET ZN A 334 1 HET FE A 335 1 HET ZN A 336 1 HET ZN A 337 1 HET ZN A 338 1 HET ZN A 339 1 HET FE A 340 1 HET FE A 341 1 HET CAC A 342 5 HET CAC A 343 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CA CALCIUM ION HETNAM ZN ZINC ION HETNAM FE FE (III) ION HETNAM CAC CACODYLATE ION HETSYN HEM HEME HETSYN CAC DIMETHYLARSINATE FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CA 2(CA 2+) FORMUL 5 ZN 7(ZN 2+) FORMUL 8 FE 3(FE 3+) FORMUL 15 CAC 2(C2 H6 AS O2 1-) FORMUL 17 HOH *350(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 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 VAL A 303 5 5 SHEET 1 A 2 PHE A 123 LEU A 124 0 SHEET 2 A 2 ILE A 276 ASP A 277 -1 O ILE A 276 N LEU A 124 SHEET 1 B 2 ALA A 173 ALA A 174 0 SHEET 2 B 2 THR A 184 PRO A 185 -1 O THR A 184 N ALA A 174 SHEET 1 C 2 GLU A 217 ALA A 218 0 SHEET 2 C 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 2.05 SSBOND 2 CYS A 14 CYS A 278 1555 1555 2.05 SSBOND 3 CYS A 34 CYS A 114 1555 1555 2.04 SSBOND 4 CYS A 242 CYS A 307 1555 1555 2.07 LINK OD2 ASP A 30 ZN ZN A 332 1555 1555 1.98 LINK OE1 GLU A 36 ZN ZN A 339 1555 1555 1.96 LINK OE2 GLU A 37 ZN ZN A 332 1555 1555 1.97 LINK OE1 GLU A 37 ZN ZN A 332 1555 1555 2.64 LINK OE2 GLU A 40 ZN ZN A 339 1555 1555 2.03 LINK O ASP A 48 CA CA A 351 1555 1555 2.48 LINK OD1 ASP A 48 CA CA A 351 1555 1555 2.40 LINK O GLY A 60 CA CA A 351 1555 1555 2.54 LINK OD1 ASP A 62 CA CA A 351 1555 1555 2.47 LINK OG SER A 64 CA CA A 351 1555 1555 2.39 LINK OD1 ASP A 69 FE FE A 341 1555 1555 2.04 LINK OE1 GLU A 83 ZN ZN A 339 1555 1555 2.03 LINK OE2 GLU A 83 ZN ZN A 339 1555 1555 2.02 LINK OE1 GLU A 83 FE FE A 340 1555 1555 2.44 LINK ND1 HIS A 95 ZN ZN A 336 1555 1555 2.08 LINK ND1 HIS A 136 ZN ZN A 338 1555 1555 2.08 LINK OE1 GLU A 140 ZN ZN A 334 1555 1555 1.95 LINK OD1 ASP A 143 ZN ZN A 334 1555 1555 1.99 LINK NE2 HIS A 169 FE HEM A 350 1555 1555 2.15 LINK O SER A 170 CA CA A 352 1555 1555 2.40 LINK OG SER A 170 CA CA A 352 1555 1555 2.56 LINK OD2 ASP A 175 ZN ZN A 337 1555 1555 2.55 LINK OD2 ASP A 175 FE FE A 340 1555 1555 2.04 LINK OD1 ASP A 187 CA CA A 352 1555 1555 2.73 LINK OD2 ASP A 187 CA CA A 352 1555 1555 2.40 LINK O THR A 189 CA CA A 352 1555 1555 2.39 LINK OG1 THR A 189 CA CA A 352 1555 1555 2.50 LINK O VAL A 192 CA CA A 352 1555 1555 2.44 LINK OD1 ASP A 194 CA CA A 352 1555 1555 2.47 LINK OD2 ASP A 237 ZN ZN A 333 1555 1555 1.96 LINK ZN ZN A 332 O HOH A 404 1555 1555 1.89 LINK ZN ZN A 333 O HOH A 405 1555 1555 2.23 LINK ZN ZN A 333 O HOH A 406 1555 1555 1.92 LINK ZN ZN A 334 O1 CAC A 342 1555 1555 1.97 LINK ZN ZN A 334 O2 CAC A 343 1555 1555 1.98 LINK FE FE A 335 O HOH A 408 1555 1555 1.97 LINK FE FE A 335 O HOH A 409 1555 1555 2.24 LINK ZN ZN A 336 O HOH A 410 1555 1555 2.30 LINK ZN ZN A 336 O HOH A 411 1555 1555 2.08 LINK ZN ZN A 336 O HOH A 412 1555 1555 2.11 LINK ZN ZN A 337 O1D HEM A 350 1555 1555 2.03 LINK ZN ZN A 338 O2 CAC A 342 1555 1555 1.99 LINK ZN ZN A 338 O1 CAC A 343 1555 1555 1.99 LINK ZN ZN A 338 O HOH A 413 1555 1555 2.19 LINK FE FE A 340 O HOH A 414 1555 1555 2.42 LINK FE FE A 341 O HOH A 415 1555 1555 2.31 LINK FE FE A 341 O HOH A 416 1555 1555 1.90 LINK FE FE A 341 O HOH A 417 1555 1555 2.37 LINK FE HEM A 350 O HOH A 595 1555 1555 2.74 LINK CA CA A 351 O HOH A 373 1555 1555 2.49 LINK CA CA A 351 O HOH A 441 1555 1555 2.36 SITE 1 AC1 25 HIS A 39 GLU A 40 LEU A 42 ARG A 43 SITE 2 AC1 25 PHE A 46 PRO A 139 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 ALA A 174 ASP A 175 SITE 5 AC1 25 LYS A 176 VAL A 177 LEU A 228 SER A 230 SITE 6 AC1 25 ZN A 337 HOH A 372 HOH A 458 HOH A 512 SITE 7 AC1 25 HOH A 595 SITE 1 AC2 6 ASP A 48 GLY A 60 ASP A 62 SER A 64 SITE 2 AC2 6 HOH A 373 HOH A 441 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 5 ASP A 30 GLU A 37 HIS A 232 ARG A 236 SITE 2 AC4 5 HOH A 404 SITE 1 AC5 4 GLU A 26 ASP A 237 HOH A 405 HOH A 406 SITE 1 AC6 4 GLU A 140 ASP A 143 CAC A 342 CAC A 343 SITE 1 AC7 4 HIS A 293 ASP A 318 HOH A 408 HOH A 409 SITE 1 AC8 4 HIS A 95 HOH A 410 HOH A 411 HOH A 412 SITE 1 AC9 3 ASP A 175 FE A 340 HEM A 350 SITE 1 BC1 5 HIS A 136 GLU A 140 CAC A 342 CAC A 343 SITE 2 BC1 5 HOH A 413 SITE 1 BC2 4 GLU A 36 GLU A 40 GLU A 83 FE A 340 SITE 1 BC3 6 GLU A 40 GLU A 83 ASP A 175 ZN A 337 SITE 2 BC3 6 ZN A 339 HOH A 414 SITE 1 BC4 5 ASP A 69 LYS A 89 HOH A 415 HOH A 416 SITE 2 BC4 5 HOH A 417 SITE 1 BC5 10 HIS A 136 VAL A 138 GLU A 140 ASP A 143 SITE 2 BC5 10 ZN A 334 ZN A 338 CAC A 343 HOH A 413 SITE 3 BC5 10 HOH A 418 HOH A 461 SITE 1 BC6 11 HIS A 136 GLU A 140 PHE A 142 ASP A 143 SITE 2 BC6 11 ZN A 334 ZN A 338 CAC A 342 HOH A 374 SITE 3 BC6 11 HOH A 413 HOH A 484 HOH A 663 CRYST1 62.683 62.683 98.217 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 0.015953 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015953 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010182 0.00000