PDB Short entry for 3PZA HEADER OXIDOREDUCTASE 14-DEC-10 3PZA TITLE FULLY REDUCED (ALL-FERROUS) PYROCOCCUS RUBRERYTHRIN AFTER A 10 SECOND TITLE 2 EXPOSURE TO PEROXIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBRERYTHRIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261 KEYWDS RUBRERYTHRIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.D.DILLARD,J.M.DEMICK,M.W.ADAMS,W.N.LANZILOTTA REVDAT 4 21-FEB-24 3PZA 1 REMARK LINK REVDAT 3 10-AUG-11 3PZA 1 JRNL VERSN REVDAT 2 29-JUN-11 3PZA 1 REMARK REVDAT 1 22-JUN-11 3PZA 0 JRNL AUTH B.D.DILLARD,J.M.DEMICK,M.W.ADAMS,W.N.LANZILOTTA JRNL TITL A CRYO-CRYSTALLOGRAPHIC TIME COURSE FOR PEROXIDE REDUCTION JRNL TITL 2 BY RUBRERYTHRIN FROM PYROCOCCUS FURIOSUS. JRNL REF J.BIOL.INORG.CHEM. V. 16 949 2011 JRNL REFN ISSN 0949-8257 JRNL PMID 21647777 JRNL DOI 10.1007/S00775-011-0795-6 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38044 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1941 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2607 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2726 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.41000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.038 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2842 ; 0.035 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3776 ; 2.239 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 5.234 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;43.021 ;24.776 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;14.707 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;14.984 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.176 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2136 ; 0.012 ; 0.021 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): 1706 ; 1.534 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2734 ; 2.634 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1136 ; 4.714 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1042 ; 8.063 ; 4.500 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3PZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062996. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : 1.0 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38044 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.025 M HEPES PH 7.0, 8% PEG 2000 MME, REMARK 280 CAPILLARY BATCH, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.30100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.30100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.79550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.30100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.30100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.79550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.30100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.30100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.79550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.30100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.30100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.79550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -269.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 104.60200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 O HOH A 202 O HOH B 230 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 13 CB GLU A 13 CG 0.259 REMARK 500 TYR B 88 CE2 TYR B 88 CD2 0.102 REMARK 500 GLU B 100 CG GLU B 100 CD 0.096 REMARK 500 TYR B 156 CE2 TYR B 156 CD2 0.095 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 GLU A 19 OE1 - CD - OE2 ANGL. DEV. = -12.0 DEGREES REMARK 500 GLU A 80 OE1 - CD - OE2 ANGL. DEV. = -13.3 DEGREES REMARK 500 GLU B 19 OE1 - CD - OE2 ANGL. DEV. = -11.8 DEGREES REMARK 500 GLU B 80 OE1 - CD - OE2 ANGL. DEV. = -14.9 DEGREES REMARK 500 LEU B 111 CB - CG - CD2 ANGL. DEV. = -10.4 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 PHE A 38 77.53 -120.00 REMARK 500 GLU A 86 -67.29 -120.16 REMARK 500 ASP A 151 -49.70 79.45 REMARK 500 PHE B 38 72.75 -119.40 REMARK 500 GLU B 86 -60.75 -123.64 REMARK 500 ASP B 151 -41.57 82.56 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 FE2 A 1 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 142 SG REMARK 620 2 CYS A 145 SG 111.2 REMARK 620 3 CYS A 157 SG 116.1 97.7 REMARK 620 4 CYS A 160 SG 99.8 122.3 110.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 174 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 19 OE2 REMARK 620 2 GLU A 19 OE1 58.5 REMARK 620 3 GLU A 52 OE2 85.5 143.7 REMARK 620 4 HIS A 55 ND1 102.9 100.4 91.8 REMARK 620 5 PEO B 1 O2 88.3 84.8 89.8 168.7 REMARK 620 6 GLU B 114 OE1 137.3 80.8 132.1 96.1 74.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 173 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 52 OE1 REMARK 620 2 PEO B 1 O1 80.6 REMARK 620 3 GLU B 80 OE2 91.0 89.1 REMARK 620 4 GLU B 80 OE1 147.6 87.4 58.6 REMARK 620 5 GLU B 114 OE2 120.8 84.8 146.0 87.6 REMARK 620 6 HIS B 117 ND1 95.0 169.7 100.3 101.0 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 173 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE1 REMARK 620 2 GLU A 80 OE2 59.2 REMARK 620 3 GLU A 114 OE2 146.9 88.2 REMARK 620 4 HIS A 117 ND1 101.5 100.3 89.6 REMARK 620 5 PEO A 172 O2 87.2 88.1 85.5 170.2 REMARK 620 6 GLU B 52 OE2 87.6 145.5 122.7 95.2 80.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 174 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 114 OE1 REMARK 620 2 PEO A 172 O1 82.9 REMARK 620 3 GLU B 19 OE1 142.4 85.7 REMARK 620 4 GLU B 19 OE2 83.8 89.4 60.3 REMARK 620 5 GLU B 52 OE1 130.0 82.8 83.4 143.4 REMARK 620 6 HIS B 55 ND1 93.7 170.1 102.4 99.5 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 172 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 142 SG REMARK 620 2 CYS B 145 SG 113.4 REMARK 620 3 CYS B 157 SG 116.4 96.3 REMARK 620 4 CYS B 160 SG 102.6 118.9 110.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEO A 172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEO B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 172 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 173 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 174 DBREF 3PZA A 2 171 UNP Q9UWP7 Q9UWP7_PYRFU 2 171 DBREF 3PZA B 2 171 UNP Q9UWP7 Q9UWP7_PYRFU 2 171 SEQRES 1 A 170 VAL VAL LYS ARG THR MET THR LYS LYS PHE LEU GLU GLU SEQRES 2 A 170 ALA PHE ALA GLY GLU SER MET ALA HIS MET ARG TYR LEU SEQRES 3 A 170 ILE PHE ALA GLU LYS ALA GLU GLN GLU GLY PHE PRO ASN SEQRES 4 A 170 ILE ALA LYS LEU PHE ARG ALA ILE ALA TYR ALA GLU PHE SEQRES 5 A 170 VAL HIS ALA LYS ASN HIS PHE ILE ALA LEU GLY LYS LEU SEQRES 6 A 170 GLY LYS THR PRO GLU ASN LEU GLN MET GLY ILE GLU GLY SEQRES 7 A 170 GLU THR PHE GLU VAL GLU GLU MET TYR PRO VAL TYR ASN SEQRES 8 A 170 LYS ALA ALA GLU PHE GLN GLY GLU LYS GLU ALA VAL ARG SEQRES 9 A 170 THR THR HIS TYR ALA LEU GLU ALA GLU LYS ILE HIS ALA SEQRES 10 A 170 GLU LEU TYR ARG LYS ALA LYS GLU LYS ALA GLU LYS GLY SEQRES 11 A 170 GLU ASP ILE GLU ILE LYS LYS VAL TYR ILE CYS PRO ILE SEQRES 12 A 170 CYS GLY TYR THR ALA VAL ASP GLU ALA PRO GLU TYR CYS SEQRES 13 A 170 PRO VAL CYS GLY ALA PRO LYS GLU LYS PHE VAL VAL PHE SEQRES 14 A 170 GLU SEQRES 1 B 170 VAL VAL LYS ARG THR MET THR LYS LYS PHE LEU GLU GLU SEQRES 2 B 170 ALA PHE ALA GLY GLU SER MET ALA HIS MET ARG TYR LEU SEQRES 3 B 170 ILE PHE ALA GLU LYS ALA GLU GLN GLU GLY PHE PRO ASN SEQRES 4 B 170 ILE ALA LYS LEU PHE ARG ALA ILE ALA TYR ALA GLU PHE SEQRES 5 B 170 VAL HIS ALA LYS ASN HIS PHE ILE ALA LEU GLY LYS LEU SEQRES 6 B 170 GLY LYS THR PRO GLU ASN LEU GLN MET GLY ILE GLU GLY SEQRES 7 B 170 GLU THR PHE GLU VAL GLU GLU MET TYR PRO VAL TYR ASN SEQRES 8 B 170 LYS ALA ALA GLU PHE GLN GLY GLU LYS GLU ALA VAL ARG SEQRES 9 B 170 THR THR HIS TYR ALA LEU GLU ALA GLU LYS ILE HIS ALA SEQRES 10 B 170 GLU LEU TYR ARG LYS ALA LYS GLU LYS ALA GLU LYS GLY SEQRES 11 B 170 GLU ASP ILE GLU ILE LYS LYS VAL TYR ILE CYS PRO ILE SEQRES 12 B 170 CYS GLY TYR THR ALA VAL ASP GLU ALA PRO GLU TYR CYS SEQRES 13 B 170 PRO VAL CYS GLY ALA PRO LYS GLU LYS PHE VAL VAL PHE SEQRES 14 B 170 GLU HET PEO A 172 2 HET FE2 A 1 1 HET FE2 A 173 1 HET FE2 A 174 1 HET PEO B 1 2 HET FE2 B 172 1 HET FE2 B 173 1 HET FE2 B 174 1 HETNAM PEO HYDROGEN PEROXIDE HETNAM FE2 FE (II) ION FORMUL 3 PEO 2(H2 O2) FORMUL 4 FE2 6(FE 2+) FORMUL 11 HOH *131(H2 O) HELIX 1 1 ARG A 5 GLY A 37 1 33 HELIX 2 2 PHE A 38 LEU A 63 1 26 HELIX 3 3 LYS A 68 GLU A 86 1 19 HELIX 4 4 GLU A 86 GLN A 98 1 13 HELIX 5 5 GLU A 100 GLU A 129 1 30 HELIX 6 6 PRO A 163 PHE A 167 5 5 HELIX 7 7 ARG B 5 GLY B 37 1 33 HELIX 8 8 PHE B 38 LEU B 63 1 26 HELIX 9 9 LYS B 68 GLU B 86 1 19 HELIX 10 10 GLU B 86 GLN B 98 1 13 HELIX 11 11 GLU B 100 LYS B 130 1 31 HELIX 12 12 PRO B 163 PHE B 167 5 5 SHEET 1 A 3 THR A 148 VAL A 150 0 SHEET 2 A 3 VAL A 139 ILE A 141 -1 N TYR A 140 O ALA A 149 SHEET 3 A 3 VAL A 168 PHE A 170 -1 O VAL A 168 N ILE A 141 SHEET 1 B 3 THR B 148 VAL B 150 0 SHEET 2 B 3 VAL B 139 ILE B 141 -1 N TYR B 140 O ALA B 149 SHEET 3 B 3 VAL B 168 PHE B 170 -1 O VAL B 168 N ILE B 141 LINK FE FE2 A 1 SG CYS A 142 1555 1555 2.31 LINK FE FE2 A 1 SG CYS A 145 1555 1555 2.29 LINK FE FE2 A 1 SG CYS A 157 1555 1555 2.29 LINK FE FE2 A 1 SG CYS A 160 1555 1555 2.33 LINK OE2 GLU A 19 FE FE2 A 174 1555 1555 2.01 LINK OE1 GLU A 19 FE FE2 A 174 1555 1555 2.14 LINK OE2 GLU A 52 FE FE2 A 174 1555 1555 1.86 LINK OE1 GLU A 52 FE FE2 B 173 1555 1555 2.01 LINK ND1 HIS A 55 FE FE2 A 174 1555 1555 2.14 LINK OE1 GLU A 80 FE FE2 A 173 1555 1555 1.98 LINK OE2 GLU A 80 FE FE2 A 173 1555 1555 2.07 LINK OE2 GLU A 114 FE FE2 A 173 1555 1555 1.91 LINK OE1 GLU A 114 FE FE2 B 174 1555 1555 1.93 LINK ND1 HIS A 117 FE FE2 A 173 1555 1555 2.13 LINK O2 PEO A 172 FE FE2 A 173 1555 1555 2.09 LINK O1 PEO A 172 FE FE2 B 174 1555 1555 2.04 LINK FE FE2 A 173 OE2 GLU B 52 1555 1555 1.95 LINK FE FE2 A 174 O2 PEO B 1 1555 1555 2.01 LINK FE FE2 A 174 OE1 GLU B 114 1555 1555 1.97 LINK O1 PEO B 1 FE FE2 B 173 1555 1555 2.13 LINK OE1 GLU B 19 FE FE2 B 174 1555 1555 2.07 LINK OE2 GLU B 19 FE FE2 B 174 1555 1555 2.10 LINK OE1 GLU B 52 FE FE2 B 174 1555 1555 1.89 LINK ND1 HIS B 55 FE FE2 B 174 1555 1555 2.12 LINK OE2 GLU B 80 FE FE2 B 173 1555 1555 2.00 LINK OE1 GLU B 80 FE FE2 B 173 1555 1555 2.09 LINK OE2 GLU B 114 FE FE2 B 173 1555 1555 1.93 LINK ND1 HIS B 117 FE FE2 B 173 1555 1555 2.13 LINK SG CYS B 142 FE FE2 B 172 1555 1555 2.33 LINK SG CYS B 145 FE FE2 B 172 1555 1555 2.34 LINK SG CYS B 157 FE FE2 B 172 1555 1555 2.34 LINK SG CYS B 160 FE FE2 B 172 1555 1555 2.30 SITE 1 AC1 7 GLU A 80 GLU A 83 GLU A 114 FE2 A 173 SITE 2 AC1 7 GLU B 19 GLU B 52 FE2 B 174 SITE 1 AC2 4 CYS A 142 CYS A 145 CYS A 157 CYS A 160 SITE 1 AC3 5 GLU A 80 GLU A 114 HIS A 117 PEO A 172 SITE 2 AC3 5 GLU B 52 SITE 1 AC4 5 GLU A 19 GLU A 52 HIS A 55 PEO B 1 SITE 2 AC4 5 GLU B 114 SITE 1 AC5 7 GLU A 19 GLU A 52 FE2 A 174 GLU B 80 SITE 2 AC5 7 GLU B 83 GLU B 114 FE2 B 173 SITE 1 AC6 4 CYS B 142 CYS B 145 CYS B 157 CYS B 160 SITE 1 AC7 5 GLU A 52 PEO B 1 GLU B 80 GLU B 114 SITE 2 AC7 5 HIS B 117 SITE 1 AC8 5 GLU A 114 PEO A 172 GLU B 19 GLU B 52 SITE 2 AC8 5 HIS B 55 CRYST1 104.602 104.602 79.591 90.00 90.00 90.00 P 42 21 2 16 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 0.009560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012564 0.00000