HEADER OXIDOREDUCTASE 19-DEC-08 3FM6 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; COMPND 7 MUTATION: 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 CLASS II (FUNGAL) PEROXIDASES, PROTOPORPHYRIN IX, ELECTRON TRANSFER, KEYWDS 2 LIGNIN PEROXIDASE, LIGNIN DEGRADATION, MANGANESE PEROXIDASE, MN- KEYWDS 3 INDEPENDENT OXIDATION PHENOLIC NON-PHENOLIC AROMATICS, MNII KEYWDS 4 OXIDATION, PEROXIDASE, POLYVALENT PEROXIDASE, OXIDOREDUCTASE, HEME, KEYWDS 5 HYDROGEN PEROXIDE, IRON, MANGANESE, METAL-BINDING, SECRETED, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR K.PIONTEK,A.T.MARTINEZ,T.CHOINOWSKI,D.A.PLATTNER REVDAT 4 01-NOV-23 3FM6 1 REMARK REVDAT 3 10-NOV-21 3FM6 1 REMARK SEQADV LINK REVDAT 2 13-JUL-11 3FM6 1 VERSN REVDAT 1 22-DEC-09 3FM6 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. 1.13 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 138206 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) : 0.100 REMARK 3 R VALUE (WORKING SET) : 0.100 REMARK 3 FREE R VALUE : 0.115 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7291 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) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10058 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.1180 REMARK 3 BIN FREE R VALUE SET COUNT : 533 REMARK 3 BIN FREE R VALUE : 0.1410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2354 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 534 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.17000 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): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.007 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.322 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2568 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2313 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3508 ; 1.409 ; 2.021 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5358 ; 0.780 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 6.174 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;37.067 ;25.463 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 375 ;11.199 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;21.501 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 383 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2944 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 514 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 581 ; 0.229 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2477 ; 0.245 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1311 ; 0.183 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1315 ; 0.093 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 618 ; 0.194 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.138 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 20 ; 0.291 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.292 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 86 ; 0.241 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.072 ; 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): 1649 ; 1.963 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 652 ; 1.647 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2631 ; 2.695 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 986 ; 2.795 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 864 ; 3.791 ; 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): 2635 ; 1.824 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 542 ;10.290 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2482 ; 4.880 ; 3.000 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3FM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 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) : 0.97992 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 145501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.13 REMARK 200 R MERGE FOR SHELL (I) : 0.13000 REMARK 200 R SYM FOR SHELL (I) : 0.15600 REMARK 200 FOR SHELL : 7.000 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 3FKG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9.0MG/ML PROTEIN IN 10MM NA-TARTRATE REMARK 280 PH 5.5, 16% PEG 8000, 100MM ZN-ACETATE, 100MM NA-CACODYLATE PH REMARK 280 5.9, 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 49.61300 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 74.41950 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 24.80650 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 OD2 ASP A 69 HZ2 LYS A 89 1.45 REMARK 500 O HOH A 818 O HOH A 851 2.14 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 ASP A 30 OD1 53.3 REMARK 620 3 GLU A 37 OE2 122.1 91.2 REMARK 620 4 HOH A 368 O 99.9 153.1 104.5 REMARK 620 N 1 2 3 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 GLU A 36 OE2 REMARK 620 2 GLU A 40 OE2 111.0 REMARK 620 3 GLU A 83 OE2 106.5 127.8 REMARK 620 4 GLU A 83 OE1 156.4 92.5 54.2 REMARK 620 5 HOH A 461 O 144.1 69.5 98.8 45.7 REMARK 620 6 HOH A 519 O 111.2 67.7 128.1 78.7 33.9 REMARK 620 N 1 2 3 4 5 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 GLU A 40 OE1 REMARK 620 2 GLU A 40 OE1 26.6 REMARK 620 3 GLU A 40 OE2 55.5 29.2 REMARK 620 4 GLU A 83 OE2 139.3 114.2 85.1 REMARK 620 5 HOH A 459 O 95.3 93.2 95.6 98.7 REMARK 620 N 1 2 3 4 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 82.0 REMARK 620 3 GLY A 60 O 69.9 94.8 REMARK 620 4 ASP A 62 OD1 136.8 85.0 70.4 REMARK 620 5 SER A 64 OG 145.6 91.8 144.5 75.5 REMARK 620 6 HOH A 493 O 101.4 169.5 95.6 98.8 79.8 REMARK 620 7 HOH A 505 O 72.2 89.2 140.9 148.6 73.9 82.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 339 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 69 OD1 REMARK 620 2 HOH A 666 O 127.2 REMARK 620 3 HOH A 700 O 91.8 117.1 REMARK 620 4 HOH A 776 O 140.7 44.5 127.1 REMARK 620 5 HOH A 877 O 144.7 66.3 56.7 73.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 338 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 83 OE1 REMARK 620 2 GLU A 83 OE1 31.0 REMARK 620 3 ASP A 175 OD1 139.5 170.3 REMARK 620 4 HOH A 461 O 47.4 78.4 92.1 REMARK 620 5 HOH A 462 O 121.9 91.4 98.2 166.2 REMARK 620 6 HOH A 463 O 86.4 92.5 87.5 79.8 91.4 REMARK 620 7 HOH A 519 O 81.6 112.1 58.9 35.3 149.4 69.1 REMARK 620 8 HOH A 675 O 101.8 127.9 46.1 60.9 121.4 51.8 28.1 REMARK 620 9 HOH A 703 O 95.2 89.0 91.1 101.0 87.9 178.4 110.9 127.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 335 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 HOH A 396 O 114.5 REMARK 620 3 HOH A 456 O 100.1 109.0 REMARK 620 4 HOH A 457 O 134.7 71.7 120.9 REMARK 620 5 HOH A 458 O 112.1 106.1 115.3 35.1 REMARK 620 N 1 2 3 4 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 128 OD2 REMARK 620 2 HOH A 555 O 94.9 REMARK 620 3 HOH A 843 O 66.4 161.3 REMARK 620 N 1 2 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 99.4 REMARK 620 3 HEM A 350 NB 96.9 89.1 REMARK 620 4 HEM A 350 NC 98.3 162.3 89.3 REMARK 620 5 HEM A 350 ND 98.1 88.4 165.0 88.6 REMARK 620 6 HOH A 619 O 177.4 79.2 85.3 83.1 79.7 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 72.1 REMARK 620 3 ASP A 187 OD1 78.9 117.1 REMARK 620 4 ASP A 187 OD2 92.0 75.9 50.4 REMARK 620 5 THR A 189 O 81.9 147.1 75.8 125.8 REMARK 620 6 THR A 189 OG1 146.6 140.6 78.0 91.6 69.3 REMARK 620 7 VAL A 192 O 85.9 82.0 149.8 157.3 76.3 102.6 REMARK 620 8 ASP A 194 OD1 140.7 69.2 125.9 85.8 130.0 72.7 81.7 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 333 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 237 OD2 REMARK 620 2 HOH A 390 O 103.6 REMARK 620 3 HOH A 608 O 149.0 45.7 REMARK 620 4 HOH A 623 O 115.4 111.8 80.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 334 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 293 NE2 REMARK 620 2 ASP A 318 OD2 90.9 REMARK 620 3 HOH A 448 O 91.9 83.8 REMARK 620 4 HOH A 454 O 169.7 97.4 95.1 REMARK 620 5 HOH A 455 O 93.0 94.9 175.0 80.3 REMARK 620 6 HOH A 677 O 84.3 175.2 95.7 87.4 86.1 REMARK 620 N 1 2 3 4 5 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 HOH A 555 O REMARK 620 2 HOH A 679 O 83.7 REMARK 620 3 HOH A 721 O 94.7 89.3 REMARK 620 N 1 2 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 FE A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN 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 FE A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE 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 GOL A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL 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: 3FKG RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE Q33N, G191E VARIANT 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: 3FMU RELATED DB: PDB REMARK 900 RECOMBINANTE VERSATILE PEROXIDASE W164S VARIANT DBREF 3FM6 A 1 331 UNP O94753 VPL2_PLEER 31 361 SEQADV 3FM6 GLN A 142 UNP O94753 PHE 172 ENGINEERED MUTATION 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 GLN 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 GLY 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 73 HET CA A 351 1 HET CA A 352 1 HET ZN A 332 1 HET ZN A 333 1 HET FE A 334 1 HET ZN A 335 1 HET ZN A 336 1 HET ZN A 337 1 HET FE A 338 1 HET FE A 339 1 HET FE A 340 1 HET FE A 341 1 HET GOL A 342 6 HET GOL A 343 6 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CA CALCIUM ION HETNAM ZN ZINC ION HETNAM FE FE (III) ION HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CA 2(CA 2+) FORMUL 5 ZN 5(ZN 2+) FORMUL 7 FE 5(FE 3+) FORMUL 15 GOL 2(C3 H8 O3) FORMUL 17 HOH *534(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 ASP A 237 1 9 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 52 SER A 53 0 SHEET 2 A 2 GLY A 57 GLY A 59 -1 O GLY A 57 N SER A 53 SHEET 1 B 2 PHE A 123 LEU A 124 0 SHEET 2 B 2 ILE A 276 ASP A 277 -1 O ILE A 276 N LEU A 124 SHEET 1 C 2 ALA A 173 ALA A 174 0 SHEET 2 C 2 THR A 184 PRO A 185 -1 O THR A 184 N ALA A 174 SHEET 1 D 2 GLU A 217 ALA A 218 0 SHEET 2 D 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 2.04 SSBOND 3 CYS A 34 CYS A 114 1555 1555 2.04 SSBOND 4 CYS A 242 CYS A 307 1555 1555 2.12 LINK OD2 ASP A 30 ZN ZN A 332 1555 1555 1.98 LINK OD1 ASP A 30 ZN ZN A 332 1555 1555 2.67 LINK OE2 GLU A 36 ZN ZN A 336 1555 1555 1.94 LINK OE2 GLU A 37 ZN ZN A 332 1555 1555 1.94 LINK OE2BGLU A 40 ZN ZN A 336 1555 1555 1.96 LINK OE1AGLU A 40 ZN ZN A 337 1555 1555 1.96 LINK OE1BGLU A 40 ZN ZN A 337 1555 1555 2.01 LINK OE2AGLU A 40 ZN ZN A 337 1555 1555 2.57 LINK O ASP A 48 CA CA A 351 1555 1555 2.48 LINK OD1 ASP A 48 CA CA A 351 1555 1555 2.34 LINK O GLY A 60 CA CA A 351 1555 1555 2.41 LINK OD1 ASP A 62 CA CA A 351 1555 1555 2.44 LINK OG SER A 64 CA CA A 351 1555 1555 2.41 LINK OD1 ASP A 69 FE FE A 339 1555 1555 2.09 LINK OE2AGLU A 83 ZN ZN A 336 1555 1555 1.94 LINK OE1AGLU A 83 ZN ZN A 336 1555 1555 2.65 LINK OE2AGLU A 83 ZN ZN A 337 1555 1555 1.99 LINK OE1AGLU A 83 FE FE A 338 1555 1555 2.59 LINK OE1BGLU A 83 FE FE A 338 1555 1555 2.07 LINK ND1 HIS A 95 ZN ZN A 335 1555 1555 2.31 LINK OD2 ASP A 128 FE FE A 341 1555 1555 2.04 LINK NE2 HIS A 169 FE HEM A 350 1555 1555 2.13 LINK O SER A 170 CA CA A 352 1555 1555 2.36 LINK OG SER A 170 CA CA A 352 1555 1555 2.49 LINK OD1 ASP A 175 FE FE A 338 1555 1555 2.03 LINK OD1 ASP A 187 CA CA A 352 1555 1555 2.69 LINK OD2 ASP A 187 CA CA A 352 1555 1555 2.43 LINK O THR A 189 CA CA A 352 1555 1555 2.40 LINK OG1 THR A 189 CA CA A 352 1555 1555 2.47 LINK O VAL A 192 CA CA A 352 1555 1555 2.41 LINK OD1 ASP A 194 CA CA A 352 1555 1555 2.44 LINK OD2 ASP A 237 ZN ZN A 333 1555 1555 2.00 LINK NE2 HIS A 293 FE FE A 334 1555 1555 2.33 LINK OD2 ASP A 318 FE FE A 334 1555 1555 2.11 LINK ZN ZN A 332 O HOH A 368 1555 1555 2.03 LINK ZN ZN A 333 O HOH A 390 1555 1555 1.98 LINK ZN ZN A 333 O HOH A 608 1555 1555 2.32 LINK ZN ZN A 333 O HOH A 623 1555 1555 2.18 LINK FE FE A 334 O HOH A 448 1555 1555 2.39 LINK FE FE A 334 O HOH A 454 1555 1555 2.09 LINK FE FE A 334 O HOH A 455 1555 1555 2.13 LINK FE FE A 334 O HOH A 677 1555 1555 1.92 LINK ZN ZN A 335 O HOH A 396 1555 1555 2.11 LINK ZN ZN A 335 O HOH A 456 1555 1555 1.66 LINK ZN ZN A 335 O HOH A 457 1555 1555 2.66 LINK ZN ZN A 335 O HOH A 458 1555 1555 1.98 LINK ZN ZN A 336 O HOH A 461 1555 1555 2.02 LINK ZN ZN A 336 O HOH A 519 1555 1555 2.34 LINK ZN ZN A 337 O HOH A 459 1555 1555 1.88 LINK FE FE A 338 O HOH A 461 1555 1555 1.82 LINK FE FE A 338 O HOH A 462 1555 1555 1.96 LINK FE FE A 338 O HOH A 463 1555 1555 2.03 LINK FE FE A 338 O HOH A 519 1555 1555 2.26 LINK FE FE A 338 O HOH A 675 1555 1555 2.42 LINK FE FE A 338 O HOH A 703 1555 1555 2.18 LINK FE FE A 339 O HOH A 666 1555 1555 2.32 LINK FE FE A 339 O HOH A 700 1555 1555 2.41 LINK FE FE A 339 O HOH A 776 1555 1555 2.40 LINK FE FE A 339 O HOH A 877 1555 1555 2.31 LINK FE FE A 340 O HOH A 555 1555 1555 2.70 LINK FE FE A 340 O HOH A 679 1555 1555 2.48 LINK FE FE A 340 O HOH A 721 1555 1555 2.07 LINK FE FE A 341 O HOH A 555 1555 1555 1.81 LINK FE FE A 341 O HOH A 843 1555 1555 2.68 LINK FE HEM A 350 O HOH A 619 1555 1555 2.65 LINK CA CA A 351 O HOH A 493 1555 1555 2.34 LINK CA CA A 351 O HOH A 505 1555 1555 2.44 SITE 1 AC1 23 HIS A 39 GLU A 40 LEU A 42 PHE A 46 SITE 2 AC1 23 GLU A 140 PRO A 141 LEU A 166 SER A 168 SITE 3 AC1 23 HIS A 169 ALA A 172 ALA A 173 ALA A 174 SITE 4 AC1 23 ASP A 175 LYS A 176 VAL A 177 PHE A 186 SITE 5 AC1 23 LEU A 228 SER A 230 GOL A 343 HOH A 619 SITE 6 AC1 23 HOH A 668 HOH A 756 HOH A 834 SITE 1 AC2 6 ASP A 48 GLY A 60 ASP A 62 SER A 64 SITE 2 AC2 6 HOH A 493 HOH A 505 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 4 ASP A 30 GLU A 37 HIS A 232 HOH A 368 SITE 1 AC5 5 GLU A 26 ASP A 237 HOH A 390 HOH A 608 SITE 2 AC5 5 HOH A 623 SITE 1 AC6 6 HIS A 293 ASP A 318 HOH A 448 HOH A 454 SITE 2 AC6 6 HOH A 455 HOH A 677 SITE 1 AC7 5 HIS A 95 HOH A 396 HOH A 456 HOH A 457 SITE 2 AC7 5 HOH A 458 SITE 1 AC8 8 GLU A 36 GLU A 40 GLU A 83 ZN A 337 SITE 2 AC8 8 FE A 338 HOH A 461 HOH A 519 HOH A 675 SITE 1 AC9 5 GLU A 36 GLU A 40 GLU A 83 ZN A 336 SITE 2 AC9 5 HOH A 459 SITE 1 BC1 9 GLU A 83 ASP A 175 ZN A 336 HOH A 461 SITE 2 BC1 9 HOH A 462 HOH A 463 HOH A 519 HOH A 675 SITE 3 BC1 9 HOH A 703 SITE 1 BC2 6 ASP A 69 LYS A 89 HOH A 666 HOH A 700 SITE 2 BC2 6 HOH A 776 HOH A 877 SITE 1 BC3 5 FE A 341 HOH A 465 HOH A 555 HOH A 679 SITE 2 BC3 5 HOH A 721 SITE 1 BC4 5 ASP A 128 FE A 340 HOH A 555 HOH A 721 SITE 2 BC4 5 HOH A 843 SITE 1 BC5 10 HIS A 136 VAL A 138 ASP A 143 ARG A 151 SITE 2 BC5 10 HOH A 529 HOH A 532 HOH A 561 HOH A 629 SITE 3 BC5 10 HOH A 711 HOH A 737 SITE 1 BC6 11 ARG A 43 PRO A 76 ALA A 77 ALA A 79 SITE 2 BC6 11 GLU A 140 PRO A 141 LYS A 176 VAL A 177 SITE 3 BC6 11 HEM A 350 HOH A 534 HOH A 866 CRYST1 63.333 63.333 99.226 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 0.015790 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010078 0.00000