HEADER DNA BINDING PROTEIN 13-NOV-08 3F8N TITLE CRYSTAL STRUCTURE OF PERR-ZN-MN CAVEAT 3F8N CHIRALITY ERROR IN ARG B 19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIDE OPERON REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PERR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: PERR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-30C(NOVAGEN) KEYWDS DNA BINDING PROTEIN, HELIX-TURN-HELIX, CYTOPLASM, DNA-BINDING, KEYWDS 2 MANGANESE, OXIDATION, REPRESSOR, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION, ZINC EXPDTA X-RAY DIFFRACTION AUTHOR D.A.K.TRAORE,J.-L.FERRER,L.JACQUAMET,V.DUARTE,J.-M.LATOUR REVDAT 4 01-NOV-23 3F8N 1 REMARK REVDAT 3 30-JUN-09 3F8N 1 JRNL REVDAT 2 23-JUN-09 3F8N 1 JRNL REVDAT 1 16-JUN-09 3F8N 0 JRNL AUTH L.JACQUAMET,D.A.K.TRAORE,J.-L.FERRER,O.PROUX,D.TESTEMALE, JRNL AUTH 2 J.-L.HAZEMANN,E.NAZARENKO,A.EL GHAZOUANI,C.CAUX-THANG, JRNL AUTH 3 V.DUARTE,J.-M.LATOUR JRNL TITL STRUCTURAL CHARACTERIZATION OF THE ACTIVE FORM OF PERR: JRNL TITL 2 INSIGHTS INTO THE METAL-INDUCED ACTIVATION OF PERR AND FUR JRNL TITL 3 PROTEINS FOR DNA BINDING JRNL REF MOL.MICROBIOL. V. 73 20 2009 JRNL REFN ISSN 0950-382X JRNL PMID 19508285 JRNL DOI 10.1111/J.1365-2958.2009.06753.X REMARK 2 REMARK 2 RESOLUTION. 3.15 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) : 3.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6725 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) : 0.277 REMARK 3 R VALUE (WORKING SET) : 0.275 REMARK 3 FREE R VALUE : 0.315 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 354 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) : 3.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 466 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3720 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 1 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.87000 REMARK 3 B22 (A**2) : 7.73000 REMARK 3 B33 (A**2) : -4.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.68000 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): 0.567 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.602 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.028 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.888 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.835 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2165 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2943 ; 1.564 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 271 ; 8.575 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;37.831 ;23.774 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;22.823 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;12.772 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 329 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1683 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1078 ; 0.299 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1444 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 72 ; 0.148 ; 0.200 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): 28 ; 0.200 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.226 ; 0.200 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): 1376 ; 0.597 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2163 ; 1.087 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 869 ; 0.699 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 780 ; 1.181 ; 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 : 4 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 83 3 REMARK 3 1 B 6 B 83 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 304 ; 0.05 ; 0.05 REMARK 3 LOOSE POSITIONAL 1 A (A): 271 ; 0.45 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 304 ; 4.79 ; 0.50 REMARK 3 LOOSE THERMAL 1 A (A**2): 271 ; 4.63 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 94 B 103 3 REMARK 3 1 A 94 A 103 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 B (A): 36 ; 0.05 ; 0.05 REMARK 3 LOOSE POSITIONAL 2 B (A): 23 ; 0.50 ; 5.00 REMARK 3 TIGHT THERMAL 2 B (A**2): 36 ; 4.11 ; 0.50 REMARK 3 LOOSE THERMAL 2 B (A**2): 23 ; 4.22 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 114 A 122 3 REMARK 3 1 B 114 B 122 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 3 A (A): 36 ; 0.04 ; 0.05 REMARK 3 LOOSE POSITIONAL 3 A (A): 28 ; 0.48 ; 5.00 REMARK 3 TIGHT THERMAL 3 A (A**2): 36 ; 5.67 ; 0.50 REMARK 3 LOOSE THERMAL 3 A (A**2): 28 ; 5.49 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 4 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 125 A 135 3 REMARK 3 1 B 125 B 135 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 4 A (A): 40 ; 0.03 ; 0.05 REMARK 3 LOOSE POSITIONAL 4 A (A): 43 ; 0.53 ; 5.00 REMARK 3 TIGHT THERMAL 4 A (A**2): 40 ; 2.11 ; 0.50 REMARK 3 LOOSE THERMAL 4 A (A**2): 43 ; 1.90 ; 10.00 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 : 1.20 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 500 SHOWS GEOMETRIC DISTORTIONS FOR SOME REMARK 3 RESIDUES THAT ARE ALSO LISTED IN REMARK 480. BUT SINCE THEY HAVE REMARK 3 BEEN ASSIGNED WITH ZERO OCCUPANCY, REMARK 500 CAN BE IGNORED FOR REMARK 3 THEM. REMARK 4 REMARK 4 3F8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050284. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6880 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.150 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10500 REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.68 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39900 REMARK 200 FOR SHELL : 3.630 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 2FE3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 1000, 0.1M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.67000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 141 REMARK 465 LYS A 142 REMARK 465 GLU A 143 REMARK 465 ASN A 144 REMARK 465 HIS A 145 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 SER B 140 REMARK 465 LYS B 141 REMARK 465 LYS B 142 REMARK 465 GLU B 143 REMARK 465 ASN B 144 REMARK 465 HIS B 145 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 14 CG CD CE NZ REMARK 470 SER A 140 OG REMARK 470 GLU B 11 CG CD OE1 OE2 REMARK 470 VAL B 103 CG1 CG2 REMARK 470 GLU B 131 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 GLU A 5 CG CD OE1 OE2 REMARK 480 LYS A 7 CB CG CD CE NZ REMARK 480 GLU A 15 CG CD OE1 OE2 REMARK 480 LYS A 45 CG CD CE REMARK 480 LYS A 50 CG CD CE NZ REMARK 480 LYS A 73 CG CD CE NZ REMARK 480 LYS A 101 CG CD CE NZ REMARK 480 GLU A 112 CB CG CD OE1 OE2 REMARK 480 LYS A 124 CG CD CE NZ REMARK 480 ARG B 19 CB CG CD REMARK 480 LYS B 73 CG CD CE NZ 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 TYR B 92 O ASP B 104 1.94 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 LYS A 7 CA LYS A 7 CB 0.527 REMARK 500 LYS A 45 CB LYS A 45 CG -0.303 REMARK 500 LYS A 45 CE LYS A 45 NZ -0.166 REMARK 500 GLU A 112 CA GLU A 112 CB 0.191 REMARK 500 ARG B 19 CA ARG B 19 CB -0.137 REMARK 500 ARG B 19 CD ARG B 19 NE 0.415 REMARK 500 LYS B 73 CB LYS B 73 CG 0.351 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 5 CA - CB - CG ANGL. DEV. = 13.7 DEGREES REMARK 500 LYS A 7 CB - CA - C ANGL. DEV. = -15.9 DEGREES REMARK 500 LYS A 45 CD - CE - NZ ANGL. DEV. = 33.8 DEGREES REMARK 500 GLU A 112 N - CA - CB ANGL. DEV. = 15.2 DEGREES REMARK 500 ARG B 19 N - CA - CB ANGL. DEV. = 19.7 DEGREES REMARK 500 ARG B 19 CA - CB - CG ANGL. DEV. = 17.0 DEGREES REMARK 500 ARG B 19 CG - CD - NE ANGL. DEV. = 35.0 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 GLU A 5 -78.00 -45.37 REMARK 500 VAL A 18 115.13 -29.03 REMARK 500 MET A 35 37.46 -71.95 REMARK 500 LYS A 50 -46.41 104.03 REMARK 500 SER A 69 36.95 -99.35 REMARK 500 ASP A 79 -100.88 41.21 REMARK 500 ALA A 80 -87.39 -90.28 REMARK 500 THR A 88 -105.49 -138.00 REMARK 500 ASP A 90 54.73 176.90 REMARK 500 HIS A 91 145.21 -177.71 REMARK 500 VAL A 103 -87.27 25.02 REMARK 500 ASP A 104 125.86 107.95 REMARK 500 PHE A 105 -55.39 -123.86 REMARK 500 HIS A 106 120.35 87.45 REMARK 500 LEU A 110 -61.63 -147.93 REMARK 500 ASP A 111 108.69 51.63 REMARK 500 GLU A 112 -138.96 30.87 REMARK 500 GLU A 114 -55.29 -17.70 REMARK 500 CYS A 136 176.25 -42.63 REMARK 500 GLN A 137 -25.34 65.25 REMARK 500 GLU A 138 -28.81 118.67 REMARK 500 VAL B 18 115.09 -24.57 REMARK 500 MET B 35 35.71 -73.82 REMARK 500 LYS B 50 -49.70 104.31 REMARK 500 SER B 69 34.84 -96.41 REMARK 500 ASP B 79 -117.01 54.81 REMARK 500 ALA B 80 -165.37 96.93 REMARK 500 ASP B 85 -108.79 -92.63 REMARK 500 PHE B 86 13.15 177.02 REMARK 500 VAL B 87 38.29 35.20 REMARK 500 SER B 89 129.91 74.76 REMARK 500 ASP B 90 134.40 179.09 REMARK 500 HIS B 91 116.86 150.84 REMARK 500 ASN B 98 -60.78 -97.50 REMARK 500 VAL B 103 138.79 -38.47 REMARK 500 ASP B 104 -78.85 -75.61 REMARK 500 PHE B 105 143.01 57.86 REMARK 500 LEU B 110 -34.51 117.48 REMARK 500 GLU B 112 -172.37 47.25 REMARK 500 GLU B 114 -64.83 -29.92 REMARK 500 CYS B 136 177.12 -50.56 REMARK 500 GLN B 137 -26.76 54.86 REMARK 500 GLU B 138 8.64 93.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 136 GLN A 137 34.71 REMARK 500 GLN A 137 GLU A 138 146.39 REMARK 500 GLU A 138 CYS A 139 30.87 REMARK 500 ASP B 79 ALA B 80 36.28 REMARK 500 CYS B 136 GLN B 137 47.63 REMARK 500 GLN B 137 GLU B 138 139.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 19 0.32 SIDE CHAIN 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 85 OD2 REMARK 620 2 ASP A 104 OD2 153.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 96 SG REMARK 620 2 CYS A 99 SG 109.9 REMARK 620 3 CYS A 136 SG 94.5 119.6 REMARK 620 4 CYS A 139 SG 115.2 108.6 108.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 85 OD1 REMARK 620 2 ASP B 104 OD2 165.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 96 SG REMARK 620 2 CYS B 99 SG 103.4 REMARK 620 3 CYS B 139 SG 94.8 114.1 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 MN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FE3 RELATED DB: PDB REMARK 900 INACTIVE APO FORM OF PERR REMARK 900 RELATED ID: 2RGV RELATED DB: PDB REMARK 900 INACTIVE OXIDIZED FORM PERR DBREF 3F8N A 1 145 UNP P71086 PERR_BACSU 1 145 DBREF 3F8N B 1 145 UNP P71086 PERR_BACSU 1 145 SEQRES 1 A 145 MET ALA ALA HIS GLU LEU LYS GLU ALA LEU GLU THR LEU SEQRES 2 A 145 LYS GLU THR GLY VAL ARG ILE THR PRO GLN ARG HIS ALA SEQRES 3 A 145 ILE LEU GLU TYR LEU VAL ASN SER MET ALA HIS PRO THR SEQRES 4 A 145 ALA ASP ASP ILE TYR LYS ALA LEU GLU GLY LYS PHE PRO SEQRES 5 A 145 ASN MET SER VAL ALA THR VAL TYR ASN ASN LEU ARG VAL SEQRES 6 A 145 PHE ARG GLU SER GLY LEU VAL LYS GLU LEU THR TYR GLY SEQRES 7 A 145 ASP ALA SER SER ARG PHE ASP PHE VAL THR SER ASP HIS SEQRES 8 A 145 TYR HIS ALA ILE CYS GLU ASN CYS GLY LYS ILE VAL ASP SEQRES 9 A 145 PHE HIS TYR PRO GLY LEU ASP GLU VAL GLU GLN LEU ALA SEQRES 10 A 145 ALA HIS VAL THR GLY PHE LYS VAL SER HIS HIS ARG LEU SEQRES 11 A 145 GLU ILE TYR GLY VAL CYS GLN GLU CYS SER LYS LYS GLU SEQRES 12 A 145 ASN HIS SEQRES 1 B 145 MET ALA ALA HIS GLU LEU LYS GLU ALA LEU GLU THR LEU SEQRES 2 B 145 LYS GLU THR GLY VAL ARG ILE THR PRO GLN ARG HIS ALA SEQRES 3 B 145 ILE LEU GLU TYR LEU VAL ASN SER MET ALA HIS PRO THR SEQRES 4 B 145 ALA ASP ASP ILE TYR LYS ALA LEU GLU GLY LYS PHE PRO SEQRES 5 B 145 ASN MET SER VAL ALA THR VAL TYR ASN ASN LEU ARG VAL SEQRES 6 B 145 PHE ARG GLU SER GLY LEU VAL LYS GLU LEU THR TYR GLY SEQRES 7 B 145 ASP ALA SER SER ARG PHE ASP PHE VAL THR SER ASP HIS SEQRES 8 B 145 TYR HIS ALA ILE CYS GLU ASN CYS GLY LYS ILE VAL ASP SEQRES 9 B 145 PHE HIS TYR PRO GLY LEU ASP GLU VAL GLU GLN LEU ALA SEQRES 10 B 145 ALA HIS VAL THR GLY PHE LYS VAL SER HIS HIS ARG LEU SEQRES 11 B 145 GLU ILE TYR GLY VAL CYS GLN GLU CYS SER LYS LYS GLU SEQRES 12 B 145 ASN HIS HET MN A 201 1 HET ZN A 202 1 HET MN B 203 1 HET ZN B 204 1 HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION FORMUL 3 MN 2(MN 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *(H2 O) HELIX 1 1 HIS A 4 GLY A 17 1 14 HELIX 2 2 THR A 21 SER A 34 1 14 HELIX 3 3 THR A 39 GLU A 48 1 10 HELIX 4 4 SER A 55 SER A 69 1 15 HELIX 5 5 GLU A 114 GLY A 122 1 9 HELIX 6 6 HIS B 4 GLY B 17 1 14 HELIX 7 7 THR B 21 SER B 34 1 14 HELIX 8 8 THR B 39 GLU B 48 1 10 HELIX 9 9 SER B 55 SER B 69 1 15 HELIX 10 10 GLU B 114 GLY B 122 1 9 SHEET 1 A 2 VAL A 72 LEU A 75 0 SHEET 2 A 2 ARG A 83 PHE A 86 -1 O ARG A 83 N LEU A 75 SHEET 1 B 4 HIS A 93 CYS A 96 0 SHEET 2 B 4 HIS A 127 VAL A 135 1 O ILE A 132 N ILE A 95 SHEET 3 B 4 LYS B 124 GLY B 134 -1 O TYR B 133 N HIS A 127 SHEET 4 B 4 HIS B 93 CYS B 96 1 N ILE B 95 O ILE B 132 SHEET 1 C 2 GLU B 74 LEU B 75 0 SHEET 2 C 2 ARG B 83 PHE B 84 -1 O ARG B 83 N LEU B 75 LINK OD2 ASP A 85 MN MN A 201 1555 1555 2.41 LINK SG CYS A 96 ZN ZN A 202 1555 1555 2.17 LINK SG CYS A 99 ZN ZN A 202 1555 1555 2.02 LINK OD2 ASP A 104 MN MN A 201 1555 1555 2.39 LINK SG CYS A 136 ZN ZN A 202 1555 1555 2.24 LINK SG CYS A 139 ZN ZN A 202 1555 1555 2.28 LINK OD1 ASP B 85 MN MN B 203 1555 1555 2.18 LINK SG CYS B 96 ZN ZN B 204 1555 1555 2.41 LINK SG CYS B 99 ZN ZN B 204 1555 1555 2.41 LINK OD2 ASP B 104 MN MN B 203 1555 1555 2.28 LINK SG CYS B 139 ZN ZN B 204 1555 1555 2.49 CISPEP 1 GLY A 49 LYS A 50 0 1.99 CISPEP 2 TYR A 77 GLY A 78 0 0.92 CISPEP 3 SER A 89 ASP A 90 0 -3.07 CISPEP 4 ASP A 90 HIS A 91 0 -7.60 CISPEP 5 PRO A 108 GLY A 109 0 -8.62 CISPEP 6 GLY A 109 LEU A 110 0 -16.53 CISPEP 7 LEU A 110 ASP A 111 0 -7.52 CISPEP 8 ASP A 111 GLU A 112 0 -4.19 CISPEP 9 VAL A 113 GLU A 114 0 4.28 CISPEP 10 GLY B 49 LYS B 50 0 2.32 CISPEP 11 TYR B 77 GLY B 78 0 1.31 CISPEP 12 SER B 89 ASP B 90 0 -17.52 CISPEP 13 ASP B 90 HIS B 91 0 -10.66 CISPEP 14 PRO B 108 GLY B 109 0 -6.02 CISPEP 15 GLY B 109 LEU B 110 0 7.13 CISPEP 16 ASP B 111 GLU B 112 0 -12.32 CISPEP 17 VAL B 113 GLU B 114 0 10.83 CISPEP 18 GLU B 138 CYS B 139 0 19.01 SITE 1 AC1 6 HIS A 37 ASP A 85 HIS A 91 HIS A 93 SITE 2 AC1 6 ASP A 104 HOH A 301 SITE 1 AC2 4 CYS A 96 CYS A 99 CYS A 136 CYS A 139 SITE 1 AC3 5 HIS B 37 ASP B 85 HIS B 91 HIS B 93 SITE 2 AC3 5 ASP B 104 SITE 1 AC4 4 CYS B 96 CYS B 99 CYS B 136 CYS B 139 CRYST1 49.300 63.340 66.730 90.00 80.41 90.00 P 1 21 1 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 0.020284 0.000000 -0.003428 0.00000 SCALE2 0.000000 0.015788 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015198 0.00000