10 20 30 40 50 60 70 80 4FEF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 30-MAY-12 4FEF
TITLE THE CRYSTAL STRUCTURES OF SEVERAL MUTANTS OF PLEUROTUS ERYNGII TITLE 2 VERSATILE PEROXIDASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: VERSATILE PEROXIDASE VPL2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-349; COMPND 5 SYNONYM: VERSATILE LIQUID PHASE PEROXIDASE 2; COMPND 6 EC: 1.11.1.16; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS ERYNGII; SOURCE 3 ORGANISM_COMMON: BOLETUS OF THE STEPPES; SOURCE 4 ORGANISM_TAXID: 5323; SOURCE 5 GENE: VPL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS LIGNIN PEROXIDASE, LIGNIN DEGRADATION, AROMATIC-SUBSTRATE BINDING, KEYWDS 2 OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.J.MATE,A.ROMERO,F.J.RUIZ-DUENAS,A.T.MARTINEZ
REVDAT 2 19-DEC-12 4FEF 1 JRNL REVDAT 1 24-OCT-12 4FEF 0
JRNL AUTH M.MORALES,M.J.MATE,A.ROMERO,M.J.MARTINEZ,A.T.MARTINEZ, JRNL AUTH 2 F.J.RUIZ-DUENAS JRNL TITL TWO OXIDATION SITES FOR LOW REDOX POTENTIAL SUBSTRATES: A JRNL TITL 2 DIRECTED MUTAGENESIS, KINETIC, AND CRYSTALLOGRAPHIC STUDY ON JRNL TITL 3 PLEUROTUS ERYNGII VERSATILE PEROXIDASE. JRNL REF J.BIOL.CHEM. V. 287 41053 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 23071108 JRNL DOI 10.1074/JBC.M112.405548
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.J.RUIZ-DUENAS,M.MORALES,M.J.MATE,A.ROMERO,M.J.MARTINEZ, REMARK 1 AUTH 2 A.T.SMITH,A.T.MARTINEZ REMARK 1 TITL SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN REMARK 1 TITL 2 ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE. REMARK 1 REF BIOCHEMISTRY V. 47 1685 2008 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 18201105 REMARK 1 DOI 10.1021/BI7020298
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28841 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) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2112 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 1.03000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.295 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2446 ; 0.034 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3349 ; 2.100 ; 2.016 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 6.399 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;36.285 ;25.340 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 351 ;13.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.519 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.216 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1906 ; 0.014 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1570 ; 1.334 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2520 ; 2.046 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 876 ; 3.427 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 829 ; 4.946 ; 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 : 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 RIDING REMARK 3 POSITIONS
REMARK 4 REMARK 4 4FEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-12. REMARK 100 THE RCSB ID CODE IS RCSB072797.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : DIAMOND (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : MAR REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30379 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 68.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2VKA REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CACODILATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 48.29200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 48.29200 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.03250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.29200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.51625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.29200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.54875 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.29200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.29200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.03250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 48.29200 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 73.54875 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 48.29200 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.51625 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 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 GLU A 191 CB CG CD OE1 OE2
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 257 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 OE1 GLU A 36 O HOH A 569 2.06 REMARK 500 OE2 GLU A 140 O3 SO4 A 404 2.12 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 82 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 187 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 257 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 96 51.93 -104.63 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 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE 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 24.9 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 709 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 724 DISTANCE = 5.98 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 HEM A 403 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 169 NE2 REMARK 620 2 HEM A 403 NA 91.6 REMARK 620 3 HEM A 403 NB 94.6 91.1 REMARK 620 4 HEM A 403 NC 94.6 173.7 88.8 REMARK 620 5 HEM A 403 ND 91.9 87.1 173.3 92.3 REMARK 620 6 HOH A 665 O 178.8 87.1 85.4 86.6 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 170 O REMARK 620 2 ASP A 187 OD2 93.2 REMARK 620 3 THR A 189 O 80.6 126.9 REMARK 620 4 VAL A 192 O 86.6 157.1 75.7 REMARK 620 5 SER A 170 OG 75.3 76.8 147.3 81.1 REMARK 620 6 ASP A 194 OD1 142.4 85.4 129.2 81.0 67.9 REMARK 620 7 THR A 189 OG1 146.5 91.3 70.3 101.5 137.9 71.1 REMARK 620 8 ASP A 187 OD1 77.5 51.2 76.2 149.6 118.6 126.7 79.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 509 O REMARK 620 2 ASP A 48 OD1 167.7 REMARK 620 3 SER A 64 OG 76.5 92.1 REMARK 620 4 GLY A 60 O 97.6 94.4 145.9 REMARK 620 5 ASP A 48 O 105.6 81.0 144.9 69.2 REMARK 620 6 ASP A 62 OD1 96.8 84.7 76.4 71.0 136.2 REMARK 620 7 HOH A 534 O 83.1 89.9 76.5 136.8 69.1 152.2 REMARK 620 N 1 2 3 4 5 6
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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FCS RELATED DB: PDB REMARK 900 THE SAME PROTEIN MUTATED AT POSITION 176 BY A GLYCINE REMARK 900 (K176G) REMARK 900 RELATED ID: 4FCN RELATED DB: PDB REMARK 900 THE SAME PROTEIN MUTATED AT POSITIONS 140 AND 176 BY REMARK 900 GLYCINES (E140G/K176G) REMARK 900 RELATED ID: 4FDQ RELATED DB: PDB REMARK 900 THE SAME PROTEIN MUTATED AT POSITION 140 BY A GLYCINE REMARK 900 (E140G)
DBREF 4FEF A 1 315 UNP O94753 VPL2_PLEER 31 345
SEQADV 4FEF GLY A 141 UNP O94753 PRO 171 ENGINEERED MUTATION SEQADV 4FEF GLU A 191 UNP O94753 GLY 221 ENGINEERED MUTATION
SEQRES 1 A 315 ALA THR CYS ASP ASP GLY ARG THR THR ALA ASN ALA ALA SEQRES 2 A 315 CYS CYS ILE LEU PHE PRO ILE LEU ASP ASP ILE GLN GLU SEQRES 3 A 315 ASN LEU PHE ASP GLY ALA GLN CYS GLY GLU GLU VAL HIS SEQRES 4 A 315 GLU SER LEU ARG LEU THR PHE HIS ASP ALA ILE GLY PHE SEQRES 5 A 315 SER PRO THR LEU GLY GLY GLY GLY ALA ASP GLY SER ILE SEQRES 6 A 315 ILE ALA PHE ASP THR ILE GLU THR ASN PHE PRO ALA ASN SEQRES 7 A 315 ALA GLY ILE ASP GLU ILE VAL SER ALA GLN LYS PRO PHE SEQRES 8 A 315 VAL ALA LYS HIS ASN ILE SER ALA GLY ASP PHE ILE GLN SEQRES 9 A 315 PHE ALA GLY ALA VAL GLY VAL SER ASN CYS PRO GLY GLY SEQRES 10 A 315 VAL ARG ILE PRO PHE PHE LEU GLY ARG PRO ASP ALA VAL SEQRES 11 A 315 ALA ALA SER PRO ASP HIS LEU VAL PRO GLU GLY PHE ASP SEQRES 12 A 315 SER VAL ASP SER ILE LEU ALA ARG MET GLY ASP ALA GLY SEQRES 13 A 315 PHE SER PRO VAL GLU VAL VAL TRP LEU LEU ALA SER HIS SEQRES 14 A 315 SER ILE ALA ALA ALA ASP LYS VAL ASP PRO SER ILE PRO SEQRES 15 A 315 GLY THR PRO PHE ASP SER THR PRO GLU VAL PHE ASP SER SEQRES 16 A 315 GLN PHE PHE ILE GLU THR GLN LEU LYS GLY ARG LEU PHE SEQRES 17 A 315 PRO GLY THR ALA ASP ASN LYS GLY GLU ALA GLN SER PRO SEQRES 18 A 315 LEU GLN GLY GLU ILE ARG LEU GLN SER ASP HIS LEU LEU SEQRES 19 A 315 ALA ARG ASP PRO GLN THR ALA CYS GLU TRP GLN SER MET SEQRES 20 A 315 VAL ASN ASN GLN PRO LYS ILE GLN ASN ARG PHE ALA ALA SEQRES 21 A 315 THR MET SER LYS MET ALA LEU LEU GLY GLN ASP LYS THR SEQRES 22 A 315 LYS LEU ILE ASP CYS SER ASP VAL ILE PRO THR PRO PRO SEQRES 23 A 315 ALA LEU VAL GLY ALA ALA HIS LEU PRO ALA GLY PHE SER SEQRES 24 A 315 LEU SER ASP VAL GLU GLN ALA CYS ALA ALA THR PRO PHE SEQRES 25 A 315 PRO ALA LEU
HET CA A 401 1 HET CA A 402 1 HET HEM A 403 43 HET SO4 A 404 5 HET GOL A 405 6
HETNAM CA CALCIUM ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL
HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 CA 2(CA 2+) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 SO4 O4 S 2- FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *313(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 THR A 201 1 7 HELIX 13 13 GLN A 229 ALA A 235 1 7 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 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 2.04 SSBOND 2 CYS A 14 CYS A 278 1555 1555 2.07 SSBOND 3 CYS A 34 CYS A 114 1555 1555 2.04 SSBOND 4 CYS A 242 CYS A 307 1555 1555 2.10
LINK NE2 HIS A 169 FE HEM A 403 1555 1555 2.09 LINK O SER A 170 CA CA A 402 1555 1555 2.35 LINK CA CA A 401 O HOH A 509 1555 1555 2.36 LINK OD2 ASP A 187 CA CA A 402 1555 1555 2.38 LINK O THR A 189 CA CA A 402 1555 1555 2.40 LINK OD1 ASP A 48 CA CA A 401 1555 1555 2.40 LINK OG SER A 64 CA CA A 401 1555 1555 2.44 LINK O VAL A 192 CA CA A 402 1555 1555 2.46 LINK O GLY A 60 CA CA A 401 1555 1555 2.46 LINK FE HEM A 403 O HOH A 665 1555 1555 2.47 LINK O ASP A 48 CA CA A 401 1555 1555 2.47 LINK OD1 ASP A 62 CA CA A 401 1555 1555 2.52 LINK OG SER A 170 CA CA A 402 1555 1555 2.53 LINK CA CA A 401 O HOH A 534 1555 1555 2.53 LINK OD1 ASP A 194 CA CA A 402 1555 1555 2.56 LINK OG1 THR A 189 CA CA A 402 1555 1555 2.56 LINK OD1 ASP A 187 CA CA A 402 1555 1555 2.68
SITE 1 AC1 6 ASP A 48 GLY A 60 ASP A 62 SER A 64 SITE 2 AC1 6 HOH A 509 HOH A 534 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 26 GLU A 36 HIS A 39 GLU A 40 LEU A 42 SITE 2 AC3 26 ARG A 43 PHE A 46 GLU A 140 GLY A 141 SITE 3 AC3 26 LEU A 165 LEU A 166 SER A 168 HIS A 169 SITE 4 AC3 26 ALA A 172 ALA A 173 ALA A 174 ASP A 175 SITE 5 AC3 26 LYS A 176 VAL A 177 PHE A 186 LEU A 228 SITE 6 AC3 26 SER A 230 HOH A 569 HOH A 639 HOH A 665 SITE 7 AC3 26 HOH A 666 HOH A 756 SITE 1 AC4 8 GLU A 140 PHE A 142 ARG A 206 HOH A 627 SITE 2 AC4 8 HOH A 735 HOH A 773 HOH A 790 HOH A 806 SITE 1 AC5 6 SER A 53 THR A 55 ARG A 151 ASP A 154 SITE 2 AC5 6 GLY A 297 HOH A 568
CRYST1 96.584 96.584 98.065 90.00 90.00 90.00 I 41 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.010354 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010354 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010197 0.00000