HEADER OXIDOREDUCTASE 07-AUG-15 5ABQ TITLE CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM TITLE 2 PLEUROTUS ERYNGII. MUTANT VPI-SS. MUTATED RESIDUES T2K, A49C, A61C, TITLE 3 D69S, T70D, S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, TITLE 4 S301K, A308R,A309K AND A314R. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VERSATILE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.16; COMPND 5 ENGINEERED: YES; COMPND 6 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 316407; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: W3110 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 F.J.MEDRANO,A.ROMERO REVDAT 2 10-JAN-24 5ABQ 1 REMARK LINK REVDAT 1 04-NOV-15 5ABQ 0 JRNL AUTH V.SAEZ-JIMENEZ,E.FERNENDEZ-FUEYO,F.J.MEDRANO,A.ROMERO, JRNL AUTH 2 A.T.MARTINEZ,F.J.RUIZ-DUENAS JRNL TITL IMPROVING THE PH-STABILITY OF VERSATILE PEROXIDASE BY JRNL TITL 2 COMPARATIVE STRUCTURAL ANALYSIS WITH A NATURALLY-STABLE JRNL TITL 3 MANGANESE PEROXIDASE. JRNL REF PLOS ONE V. 10 40984 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26496708 JRNL DOI 10.1371/JOURNAL.PONE.0140984 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.300 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.9170 - 4.7669 0.99 1390 156 0.2216 0.2753 REMARK 3 2 4.7669 - 3.7843 1.00 1317 146 0.2233 0.2563 REMARK 3 3 3.7843 - 3.3061 1.00 1297 144 0.2408 0.3006 REMARK 3 4 3.3061 - 3.0039 1.00 1295 144 0.2558 0.2911 REMARK 3 5 3.0039 - 2.7887 1.00 1292 144 0.2698 0.3280 REMARK 3 6 2.7887 - 2.6243 1.00 1279 142 0.2938 0.3712 REMARK 3 7 2.6243 - 2.4929 1.00 1272 141 0.2986 0.3503 REMARK 3 8 2.4929 - 2.3843 0.99 1267 141 0.2957 0.3944 REMARK 3 9 2.3843 - 2.2926 0.99 1238 137 0.3169 0.3759 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 2425 REMARK 3 ANGLE : 0.772 3311 REMARK 3 CHIRALITY : 0.030 362 REMARK 3 PLANARITY : 0.004 444 REMARK 3 DIHEDRAL : 14.653 860 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 27 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3260 16.4111 3.6129 REMARK 3 T TENSOR REMARK 3 T11: 1.0149 T22: 0.5343 REMARK 3 T33: 0.5388 T12: -0.0179 REMARK 3 T13: 0.2522 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 4.3849 L22: 4.4781 REMARK 3 L33: 0.9856 L12: 0.6094 REMARK 3 L13: -0.7849 L23: -1.5313 REMARK 3 S TENSOR REMARK 3 S11: 0.5005 S12: 0.8817 S13: 0.2295 REMARK 3 S21: -1.2490 S22: 0.1807 S23: -0.2406 REMARK 3 S31: -0.7653 S32: 0.5321 S33: -0.2214 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 28 THROUGH 81 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1231 1.0473 20.8276 REMARK 3 T TENSOR REMARK 3 T11: 0.2337 T22: 0.3048 REMARK 3 T33: 0.3434 T12: 0.0235 REMARK 3 T13: 0.0890 T23: -0.0582 REMARK 3 L TENSOR REMARK 3 L11: 2.4443 L22: 5.7804 REMARK 3 L33: 3.3584 L12: -2.0763 REMARK 3 L13: -0.2497 L23: 0.0793 REMARK 3 S TENSOR REMARK 3 S11: -0.1515 S12: -0.1356 S13: -0.4378 REMARK 3 S21: -0.5515 S22: 0.1113 S23: -0.4845 REMARK 3 S31: -0.3769 S32: 0.3155 S33: 0.1052 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 82 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9247 9.9518 15.6332 REMARK 3 T TENSOR REMARK 3 T11: 0.4844 T22: 0.2799 REMARK 3 T33: 0.3097 T12: 0.0135 REMARK 3 T13: 0.0745 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 4.0413 L22: 5.8482 REMARK 3 L33: 4.7668 L12: -0.3460 REMARK 3 L13: -2.9448 L23: 1.9131 REMARK 3 S TENSOR REMARK 3 S11: 0.0522 S12: 0.1080 S13: 0.6746 REMARK 3 S21: -1.1658 S22: 0.0372 S23: -0.4296 REMARK 3 S31: -0.3525 S32: 0.3560 S33: -0.1424 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 114 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.8850 -6.9739 16.8976 REMARK 3 T TENSOR REMARK 3 T11: 0.2245 T22: 0.2376 REMARK 3 T33: 0.3074 T12: 0.0005 REMARK 3 T13: 0.0429 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.3978 L22: 5.2819 REMARK 3 L33: 1.8708 L12: 0.4871 REMARK 3 L13: -0.5065 L23: 0.0299 REMARK 3 S TENSOR REMARK 3 S11: 0.0050 S12: -0.0619 S13: 0.2604 REMARK 3 S21: -0.3402 S22: 0.0848 S23: -0.3455 REMARK 3 S31: 0.0205 S32: 0.1135 S33: -0.0845 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 212 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.9058 -9.7641 17.3729 REMARK 3 T TENSOR REMARK 3 T11: 0.4529 T22: 0.6191 REMARK 3 T33: 1.1163 T12: 0.0359 REMARK 3 T13: 0.1784 T23: -0.1343 REMARK 3 L TENSOR REMARK 3 L11: 2.7440 L22: 3.4001 REMARK 3 L33: 3.3950 L12: 2.0668 REMARK 3 L13: 0.0859 L23: 1.3975 REMARK 3 S TENSOR REMARK 3 S11: 0.3668 S12: -0.0160 S13: 0.2048 REMARK 3 S21: 0.0681 S22: 0.0650 S23: -1.5548 REMARK 3 S31: 0.3363 S32: 0.3501 S33: -0.3086 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 213 THROUGH 250 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4629 -16.3805 17.4509 REMARK 3 T TENSOR REMARK 3 T11: 0.4211 T22: 0.3985 REMARK 3 T33: 1.0484 T12: 0.0194 REMARK 3 T13: 0.2630 T23: -0.0752 REMARK 3 L TENSOR REMARK 3 L11: 3.6110 L22: 3.2767 REMARK 3 L33: 1.2184 L12: 0.3571 REMARK 3 L13: 1.0459 L23: -0.7739 REMARK 3 S TENSOR REMARK 3 S11: -0.4329 S12: -0.0636 S13: -0.1512 REMARK 3 S21: -0.4538 S22: 0.0947 S23: -1.4981 REMARK 3 S31: -0.4399 S32: 0.3022 S33: 0.2301 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 251 THROUGH 278 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.3917 -3.5959 5.2985 REMARK 3 T TENSOR REMARK 3 T11: 1.0001 T22: 0.4469 REMARK 3 T33: 0.2899 T12: 0.0515 REMARK 3 T13: -0.2649 T23: -0.0781 REMARK 3 L TENSOR REMARK 3 L11: 3.4941 L22: 2.3828 REMARK 3 L33: 2.6762 L12: -0.5700 REMARK 3 L13: -0.4472 L23: 1.3077 REMARK 3 S TENSOR REMARK 3 S11: -0.5844 S12: 0.4319 S13: -0.0593 REMARK 3 S21: -0.4073 S22: 0.0498 S23: 0.7133 REMARK 3 S31: -0.4132 S32: -0.4076 S33: -0.4660 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 279 THROUGH 314 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.1245 -12.6754 6.2030 REMARK 3 T TENSOR REMARK 3 T11: 0.9066 T22: 0.6165 REMARK 3 T33: 1.2979 T12: 0.1160 REMARK 3 T13: 0.3651 T23: -0.1082 REMARK 3 L TENSOR REMARK 3 L11: 0.8885 L22: 0.4815 REMARK 3 L33: 0.9118 L12: -0.0821 REMARK 3 L13: -0.7388 L23: 0.3679 REMARK 3 S TENSOR REMARK 3 S11: 0.1918 S12: 0.4495 S13: -0.5547 REMARK 3 S21: -0.2198 S22: -0.0508 S23: -0.6889 REMARK 3 S31: 0.0811 S32: 0.2536 S33: -0.2712 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5ABQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1290064633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-14 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12985 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3FMU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE BUFFER AT PH 5.4, REMARK 280 12% PEG 4000 AND 0.2 M CALCIUM ACETATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.95750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.90900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.38150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.90900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.95750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.38150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 ALA A 1 REMARK 465 LYS A 2 REMARK 465 LEU A 315 REMARK 465 THR A 316 REMARK 465 ALA A 317 REMARK 465 ASP A 318 REMARK 465 PRO A 319 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 ARG A 308 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 ARG A 314 CG CD NE CZ NH1 NH2 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 CB CYS A 3 SG CYS A 15 2.09 REMARK 500 OD1 ASP A 280 O HOH A 2056 2.17 REMARK 500 O LYS A 204 NH1 ARG A 206 2.18 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 ASP A 4 -135.25 -109.25 REMARK 500 LEU A 28 -32.69 -143.59 REMARK 500 CYS A 34 55.57 -102.18 REMARK 500 PHE A 68 54.28 -114.88 REMARK 500 ASP A 194 -161.19 -129.45 REMARK 500 ASP A 213 117.88 -36.92 REMARK 500 LYS A 215 112.32 -31.47 REMARK 500 THR A 240 -11.65 -141.75 REMARK 500 VAL A 248 83.73 -68.96 REMARK 500 ASN A 249 -40.54 170.97 REMARK 500 LEU A 268 109.42 -59.62 REMARK 500 GLN A 270 -18.70 -147.00 REMARK 500 ASP A 271 174.19 71.75 REMARK 500 LYS A 272 -64.77 -105.29 REMARK 500 VAL A 289 62.04 -103.99 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2064 DISTANCE = 6.04 ANGSTROMS 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 A1315 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 48 O REMARK 620 2 ASP A 48 OD1 79.0 REMARK 620 3 GLY A 60 O 67.8 88.4 REMARK 620 4 ASP A 62 OD1 133.5 84.8 68.5 REMARK 620 5 SER A 64 OG 149.1 91.8 142.1 73.8 REMARK 620 6 HOH A2008 O 73.8 87.1 141.5 148.7 76.3 REMARK 620 7 HOH A2011 O 99.9 177.6 93.2 97.5 88.1 90.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1317 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 96 OD1 REMARK 620 2 GLU A 140 OE1 82.4 REMARK 620 3 ASP A 143 OD1 82.4 82.7 REMARK 620 4 ASP A 143 OD2 132.7 96.2 50.9 REMARK 620 5 HOH A2028 O 138.2 105.6 138.8 87.9 REMARK 620 6 HOH A2030 O 69.3 89.4 151.4 157.7 69.8 REMARK 620 7 HOH A2031 O 82.2 164.5 93.1 92.6 87.4 87.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 169 NE2 REMARK 620 2 HEM A 500 NA 91.1 REMARK 620 3 HEM A 500 NB 91.2 89.8 REMARK 620 4 HEM A 500 NC 91.7 177.1 89.3 REMARK 620 5 HEM A 500 ND 96.5 89.8 172.3 90.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1316 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 170 OG REMARK 620 2 SER A 170 O 77.3 REMARK 620 3 ASP A 187 OD1 121.1 70.8 REMARK 620 4 ASP A 187 OD2 84.7 83.7 44.4 REMARK 620 5 THR A 189 OG1 138.5 144.2 85.5 98.0 REMARK 620 6 THR A 189 O 145.9 83.8 77.5 121.3 64.7 REMARK 620 7 VAL A 192 O 79.9 82.9 139.8 161.4 100.4 69.7 REMARK 620 8 ASP A 194 OD1 69.0 145.2 135.0 101.2 69.9 120.2 82.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1318 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 297 O REMARK 620 2 HOH A2062 O 92.0 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 CA A 1315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1318 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ABN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM REMARK 900 PLEUROTUS ERYNGII. MUTANT VPI. MUTATED RESIDUES D69S, T70D, S86E, REMARK 900 D146T, Q202L, H232E, Q239R AND S301K . REMARK 900 RELATED ID: 5ABO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF FUNGAL VERSATILE PEROXIDASE FROM REMARK 900 PLEUROTUS ERYNGII. MUTANT VPI-BR. MUTATED RESIDUES T2K, D69S, T70D, REMARK 900 S86E, A131K, D146T, Q202L, Q219K, H232E, Q239R, L288R, S301K, A308R, REMARK 900 A309K AND A314R. DBREF 5ABQ A 3 331 UNP O94753 VPL2_PLEER 33 361 SEQADV 5ABQ ALA A 1 UNP O94753 EXPRESSION TAG SEQADV 5ABQ LYS A 2 UNP O94753 EXPRESSION TAG SEQADV 5ABQ CYS A 49 UNP O94753 ALA 79 ENGINEERED MUTATION SEQADV 5ABQ CYS A 61 UNP O94753 ALA 91 ENGINEERED MUTATION SEQADV 5ABQ SER A 69 UNP O94753 ASP 99 ENGINEERED MUTATION SEQADV 5ABQ ASP A 70 UNP O94753 THR 100 ENGINEERED MUTATION SEQADV 5ABQ GLU A 86 UNP O94753 SER 116 ENGINEERED MUTATION SEQADV 5ABQ THR A 146 UNP O94753 ASP 176 ENGINEERED MUTATION SEQADV 5ABQ LEU A 202 UNP O94753 GLN 232 ENGINEERED MUTATION SEQADV 5ABQ GLU A 232 UNP O94753 HIS 262 ENGINEERED MUTATION SEQADV 5ABQ ARG A 239 UNP O94753 GLN 269 ENGINEERED MUTATION SEQADV 5ABQ LYS A 301 UNP O94753 SER 331 ENGINEERED MUTATION SEQRES 1 A 331 ALA LYS 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 CYS ILE GLY PHE SEQRES 5 A 331 SER PRO THR LEU GLY GLY GLY GLY CYS ASP GLY SER ILE SEQRES 6 A 331 ILE ALA PHE SER ASP ILE GLU THR ASN PHE PRO ALA ASN SEQRES 7 A 331 ALA GLY ILE ASP GLU ILE VAL GLU 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 LYS ALA SER PRO ASP HIS LEU VAL PRO GLU PRO PHE ASP SEQRES 12 A 331 SER VAL THR 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 LEU 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 GLU LEU LEU SEQRES 19 A 331 ALA ARG ASP PRO ARG 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 LYS ASP VAL GLU GLN ALA CYS ARG LYS THR PRO PHE SEQRES 25 A 331 PRO ARG LEU THR ALA ASP PRO GLY PRO VAL THR SER VAL SEQRES 26 A 331 PRO PRO VAL PRO GLY SER HET HEM A 500 43 HET CA A1315 1 HET CA A1316 1 HET CA A1317 1 HET CA A1318 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CA CALCIUM ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *65(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 SER A 112 1 15 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 LEU A 202 1 8 HELIX 13 13 GLN A 229 ASP A 237 1 9 HELIX 14 14 THR A 240 VAL A 248 1 9 HELIX 15 15 ASN A 250 LEU A 267 1 18 HELIX 16 16 SER A 279 ILE A 282 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 2.03 SSBOND 2 CYS A 14 CYS A 278 1555 1555 2.03 SSBOND 3 CYS A 34 CYS A 114 1555 1555 2.03 SSBOND 4 CYS A 49 CYS A 61 1555 1555 2.03 SSBOND 5 CYS A 242 CYS A 307 1555 1555 2.03 LINK O ASP A 48 CA CA A1315 1555 1555 2.50 LINK OD1 ASP A 48 CA CA A1315 1555 1555 2.46 LINK O GLY A 60 CA CA A1315 1555 1555 2.42 LINK OD1 ASP A 62 CA CA A1315 1555 1555 2.52 LINK OG SER A 64 CA CA A1315 1555 1555 2.47 LINK OD1 ASN A 96 CA CA A1317 3445 1555 2.48 LINK OE1 GLU A 140 CA CA A1317 1555 1555 2.54 LINK OD1 ASP A 143 CA CA A1317 1555 1555 2.67 LINK OD2 ASP A 143 CA CA A1317 1555 1555 2.42 LINK NE2 HIS A 169 FE HEM A 500 1555 1555 2.68 LINK OG SER A 170 CA CA A1316 1555 1555 2.50 LINK O SER A 170 CA CA A1316 1555 1555 2.42 LINK OD1 ASP A 187 CA CA A1316 1555 1555 3.11 LINK OD2 ASP A 187 CA CA A1316 1555 1555 2.46 LINK OG1 THR A 189 CA CA A1316 1555 1555 2.58 LINK O THR A 189 CA CA A1316 1555 1555 2.45 LINK O VAL A 192 CA CA A1316 1555 1555 2.50 LINK OD1 ASP A 194 CA CA A1316 1555 1555 2.48 LINK O GLY A 297 CA CA A1318 1555 1555 2.54 LINK CA CA A1315 O HOH A2008 1555 1555 2.66 LINK CA CA A1315 O HOH A2011 1555 1555 2.44 LINK CA CA A1317 O HOH A2028 1555 1555 2.55 LINK CA CA A1317 O HOH A2030 1555 1555 2.55 LINK CA CA A1317 O HOH A2031 1555 1555 2.61 LINK CA CA A1318 O HOH A2062 1555 1555 2.60 SITE 1 AC1 6 ASP A 48 GLY A 60 ASP A 62 SER A 64 SITE 2 AC1 6 HOH A2008 HOH A2011 SITE 1 AC2 5 SER A 170 ASP A 187 THR A 189 VAL A 192 SITE 2 AC2 5 ASP A 194 SITE 1 AC3 23 HIS A 39 GLU A 40 LEU A 42 ARG A 43 SITE 2 AC3 23 PHE A 46 PRO A 139 GLU A 140 PRO A 141 SITE 3 AC3 23 LEU A 165 LEU A 166 SER A 168 HIS A 169 SITE 4 AC3 23 ALA A 172 ALA A 173 ALA A 174 ASP A 175 SITE 5 AC3 23 LYS A 176 VAL A 177 PHE A 186 LEU A 228 SITE 6 AC3 23 SER A 230 HOH A2006 HOH A2007 SITE 1 AC4 6 ASN A 96 GLU A 140 ASP A 143 HOH A2028 SITE 2 AC4 6 HOH A2030 HOH A2031 SITE 1 AC5 2 GLY A 297 HOH A2062 CRYST1 45.915 68.763 87.818 90.00 90.00 90.00 P 21 21 21 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 0.021779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011387 0.00000