HEADER OXIDOREDUCTASE 09-NOV-08 3F7J TITLE B.SUBTILIS YVGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: YVGN PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE REDUCTASE PROTEIN, YVGN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YVGN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ALDO-KETO REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.F.ZHOU,J.LEI,Y.H.LIANG,X.-D.SU REVDAT 5 27-DEC-23 3F7J 1 REMARK LINK REVDAT 4 29-JAN-14 3F7J 1 JRNL REVDAT 3 13-JUL-11 3F7J 1 VERSN REVDAT 2 24-FEB-09 3F7J 1 VERSN REVDAT 1 25-NOV-08 3F7J 0 SPRSDE 25-NOV-08 3F7J 3B3E JRNL AUTH J.LEI,Y.F.ZHOU,L.F.LI,X.-D.SU JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSES OF YVGN AND YTBE FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF PROTEIN SCI. V. 18 1792 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19585557 JRNL DOI 10.1002/PRO.178 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 59998 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1813 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4191 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 103 REMARK 3 BIN FREE R VALUE : 0.4240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 528 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : -0.58000 REMARK 3 B33 (A**2) : -0.52000 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): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.252 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4600 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6208 ; 1.745 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 556 ; 6.257 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;38.091 ;25.526 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 857 ;16.934 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;24.367 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 673 ; 0.197 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3486 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2756 ; 0.280 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3153 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 512 ; 0.251 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.329 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 39 ; 0.316 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.352 ; 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): 2781 ; 0.596 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4447 ; 1.037 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1835 ; 1.986 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1759 ; 3.094 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 276 REMARK 3 ORIGIN FOR THE GROUP (A): -17.6483 10.2456 -22.1653 REMARK 3 T TENSOR REMARK 3 T11: -0.1951 T22: -0.1463 REMARK 3 T33: -0.1248 T12: 0.0146 REMARK 3 T13: -0.0060 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.6201 L22: 2.4586 REMARK 3 L33: 2.8088 L12: 0.2249 REMARK 3 L13: -0.1640 L23: 0.8706 REMARK 3 S TENSOR REMARK 3 S11: -0.0337 S12: -0.0099 S13: 0.0245 REMARK 3 S21: -0.2088 S22: -0.0226 S23: 0.0713 REMARK 3 S31: 0.1550 S32: -0.0793 S33: 0.0563 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 276 REMARK 3 ORIGIN FOR THE GROUP (A): -18.4220 41.2470 -6.4538 REMARK 3 T TENSOR REMARK 3 T11: -0.1700 T22: -0.1499 REMARK 3 T33: -0.1154 T12: -0.0022 REMARK 3 T13: 0.0032 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.5748 L22: 2.2499 REMARK 3 L33: 2.9142 L12: -0.3153 REMARK 3 L13: 0.1236 L23: 1.0960 REMARK 3 S TENSOR REMARK 3 S11: 0.0214 S12: -0.0057 S13: 0.0082 REMARK 3 S21: -0.1480 S22: -0.0446 S23: 0.0456 REMARK 3 S31: -0.1837 S32: -0.0503 S33: 0.0232 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 4 REMARK 4 3F7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60078 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 66.872 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3080 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : 0.49300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 0.4M SODIUM NITRATE, 40% REMARK 280 PEG3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 39.82800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.53750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.82800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 61.53750 REMARK 290 SMTRY3 4 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 N NO3 A 281 LIES ON A SPECIAL POSITION. REMARK 375 O2 NO3 A 281 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 661 LIES ON A SPECIAL POSITION. 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 569 O HOH B 371 1.45 REMARK 500 O HOH B 301 O HOH B 467 1.58 REMARK 500 CD1 ILE B 245 O HOH B 523 1.63 REMARK 500 CG GLN B 194 O HOH B 463 1.85 REMARK 500 N ASN B 142 O HOH B 521 1.90 REMARK 500 O HOH A 302 O HOH A 641 1.90 REMARK 500 O ASP A 244 O HOH A 643 1.91 REMARK 500 CG GLU B 165 O HOH B 645 1.93 REMARK 500 CD GLU B 165 O HOH B 552 1.94 REMARK 500 O HOH A 329 O HOH A 544 1.96 REMARK 500 O HOH A 516 O HOH A 530 1.98 REMARK 500 O HOH B 446 O HOH B 637 2.02 REMARK 500 O HOH A 373 O HOH A 480 2.06 REMARK 500 CD2 LEU B 274 O HOH A 660 2.08 REMARK 500 O TYR B 105 O HOH B 469 2.09 REMARK 500 OE1 GLU B 165 O HOH B 552 2.10 REMARK 500 O HOH B 358 O HOH B 656 2.11 REMARK 500 O HOH B 301 O HOH B 379 2.11 REMARK 500 CB THR A 204 O HOH A 482 2.11 REMARK 500 O PRO B 191 O HOH B 524 2.12 REMARK 500 O HOH B 365 O HOH B 623 2.12 REMARK 500 O HOH A 377 O HOH A 570 2.12 REMARK 500 OH TYR A 54 O HOH A 431 2.13 REMARK 500 NH2 ARG B 100 O HOH B 353 2.13 REMARK 500 OE1 GLU B 83 O HOH B 593 2.15 REMARK 500 O GLN B 163 O HOH B 521 2.16 REMARK 500 CG1 VAL B 164 O HOH B 521 2.16 REMARK 500 O MET B 160 O HOH B 457 2.16 REMARK 500 CG GLU B 249 O HOH B 670 2.17 REMARK 500 CB LEU B 103 O HOH B 535 2.18 REMARK 500 O HOH A 350 O HOH A 563 2.18 REMARK 500 CD GLU B 58 O HOH B 607 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 618 O HOH A 618 2455 1.25 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 VAL A 140 CG1 - CB - CG2 ANGL. DEV. = 10.9 DEGREES REMARK 500 VAL A 140 CA - CB - CG1 ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG B 176 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 176 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ASP A 117 24.99 -158.71 REMARK 500 LYS B 26 27.61 47.80 REMARK 500 LYS B 116 -63.76 -94.17 REMARK 500 ASP B 117 28.21 -151.30 REMARK 500 ASP B 264 55.51 35.06 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 K B 281 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NO3 A 280 O3 REMARK 620 2 NO3 A 280 O2 44.8 REMARK 620 3 ASN B 82 OD1 124.8 80.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 282 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 486 O REMARK 620 2 HOH B 668 O 139.9 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 NO3 A 277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 279 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 277 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 279 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 282 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B3D RELATED DB: PDB REMARK 900 APOYTBE REMARK 900 RELATED ID: 3B3F RELATED DB: PDB REMARK 900 HOLOYVGN DBREF 3F7J A 1 276 UNP O32210 O32210_BACSU 1 276 DBREF 3F7J B 1 276 UNP O32210 O32210_BACSU 1 276 SEQRES 1 A 276 MET PRO THR SER LEU LYS ASP THR VAL LYS LEU HIS ASN SEQRES 2 A 276 GLY VAL GLU MET PRO TRP PHE GLY LEU GLY VAL PHE LYS SEQRES 3 A 276 VAL GLU ASN GLY ASN GLU ALA THR GLU SER VAL LYS ALA SEQRES 4 A 276 ALA ILE LYS ASN GLY TYR ARG SER ILE ASP THR ALA ALA SEQRES 5 A 276 ILE TYR LYS ASN GLU GLU GLY VAL GLY ILE GLY ILE LYS SEQRES 6 A 276 GLU SER GLY VAL ALA ARG GLU GLU LEU PHE ILE THR SER SEQRES 7 A 276 LYS VAL TRP ASN GLU ASP GLN GLY TYR GLU THR THR LEU SEQRES 8 A 276 ALA ALA PHE GLU LYS SER LEU GLU ARG LEU GLN LEU ASP SEQRES 9 A 276 TYR LEU ASP LEU TYR LEU ILE HIS TRP PRO GLY LYS ASP SEQRES 10 A 276 LYS TYR LYS ASP THR TRP ARG ALA LEU GLU LYS LEU TYR SEQRES 11 A 276 LYS ASP GLY LYS ILE ARG ALA ILE GLY VAL SER ASN PHE SEQRES 12 A 276 GLN VAL HIS HIS LEU GLU GLU LEU LEU LYS ASP ALA GLU SEQRES 13 A 276 ILE LYS PRO MET VAL ASN GLN VAL GLU PHE HIS PRO ARG SEQRES 14 A 276 LEU THR GLN LYS GLU LEU ARG ASP TYR CYS LYS GLY GLN SEQRES 15 A 276 GLY ILE GLN LEU GLU ALA TRP SER PRO LEU MET GLN GLY SEQRES 16 A 276 GLN LEU LEU ASP ASN GLU VAL LEU THR GLN ILE ALA GLU SEQRES 17 A 276 LYS HIS ASN LYS SER VAL ALA GLN VAL ILE LEU ARG TRP SEQRES 18 A 276 ASP LEU GLN HIS GLY VAL VAL THR ILE PRO LYS SER ILE SEQRES 19 A 276 LYS GLU HIS ARG ILE ILE GLU ASN ALA ASP ILE PHE ASP SEQRES 20 A 276 PHE GLU LEU SER GLN GLU ASP MET ASP LYS ILE ASP ALA SEQRES 21 A 276 LEU ASN LYS ASP GLU ARG VAL GLY PRO ASN PRO ASP GLU SEQRES 22 A 276 LEU LEU PHE SEQRES 1 B 276 MET PRO THR SER LEU LYS ASP THR VAL LYS LEU HIS ASN SEQRES 2 B 276 GLY VAL GLU MET PRO TRP PHE GLY LEU GLY VAL PHE LYS SEQRES 3 B 276 VAL GLU ASN GLY ASN GLU ALA THR GLU SER VAL LYS ALA SEQRES 4 B 276 ALA ILE LYS ASN GLY TYR ARG SER ILE ASP THR ALA ALA SEQRES 5 B 276 ILE TYR LYS ASN GLU GLU GLY VAL GLY ILE GLY ILE LYS SEQRES 6 B 276 GLU SER GLY VAL ALA ARG GLU GLU LEU PHE ILE THR SER SEQRES 7 B 276 LYS VAL TRP ASN GLU ASP GLN GLY TYR GLU THR THR LEU SEQRES 8 B 276 ALA ALA PHE GLU LYS SER LEU GLU ARG LEU GLN LEU ASP SEQRES 9 B 276 TYR LEU ASP LEU TYR LEU ILE HIS TRP PRO GLY LYS ASP SEQRES 10 B 276 LYS TYR LYS ASP THR TRP ARG ALA LEU GLU LYS LEU TYR SEQRES 11 B 276 LYS ASP GLY LYS ILE ARG ALA ILE GLY VAL SER ASN PHE SEQRES 12 B 276 GLN VAL HIS HIS LEU GLU GLU LEU LEU LYS ASP ALA GLU SEQRES 13 B 276 ILE LYS PRO MET VAL ASN GLN VAL GLU PHE HIS PRO ARG SEQRES 14 B 276 LEU THR GLN LYS GLU LEU ARG ASP TYR CYS LYS GLY GLN SEQRES 15 B 276 GLY ILE GLN LEU GLU ALA TRP SER PRO LEU MET GLN GLY SEQRES 16 B 276 GLN LEU LEU ASP ASN GLU VAL LEU THR GLN ILE ALA GLU SEQRES 17 B 276 LYS HIS ASN LYS SER VAL ALA GLN VAL ILE LEU ARG TRP SEQRES 18 B 276 ASP LEU GLN HIS GLY VAL VAL THR ILE PRO LYS SER ILE SEQRES 19 B 276 LYS GLU HIS ARG ILE ILE GLU ASN ALA ASP ILE PHE ASP SEQRES 20 B 276 PHE GLU LEU SER GLN GLU ASP MET ASP LYS ILE ASP ALA SEQRES 21 B 276 LEU ASN LYS ASP GLU ARG VAL GLY PRO ASN PRO ASP GLU SEQRES 22 B 276 LEU LEU PHE HET NO3 A 277 4 HET NO3 A 278 4 HET NO3 A 279 4 HET NO3 A 280 4 HET NO3 A 281 4 HET NO3 B 277 4 HET NO3 B 278 4 HET NO3 B 279 4 HET NO3 B 280 4 HET K B 281 1 HET K B 282 1 HETNAM NO3 NITRATE ION HETNAM K POTASSIUM ION FORMUL 3 NO3 9(N O3 1-) FORMUL 12 K 2(K 1+) FORMUL 14 HOH *528(H2 O) HELIX 1 1 GLY A 30 ASN A 43 1 14 HELIX 2 2 ALA A 51 LYS A 55 5 5 HELIX 3 3 ASN A 56 GLY A 68 1 13 HELIX 4 4 ALA A 70 LEU A 74 5 5 HELIX 5 5 TRP A 81 GLN A 85 5 5 HELIX 6 6 GLY A 86 GLN A 102 1 17 HELIX 7 7 LYS A 118 ASP A 132 1 15 HELIX 8 8 GLN A 144 ALA A 155 1 12 HELIX 9 9 GLN A 172 GLY A 183 1 12 HELIX 10 10 LEU A 192 GLN A 196 5 5 HELIX 11 11 ASN A 200 ASN A 211 1 12 HELIX 12 12 SER A 213 HIS A 225 1 13 HELIX 13 13 LYS A 235 ALA A 243 1 9 HELIX 14 14 SER A 251 ALA A 260 1 10 HELIX 15 15 ASN B 29 ASN B 43 1 15 HELIX 16 16 ALA B 51 LYS B 55 5 5 HELIX 17 17 ASN B 56 GLY B 68 1 13 HELIX 18 18 ALA B 70 LEU B 74 5 5 HELIX 19 19 TRP B 81 GLN B 85 5 5 HELIX 20 20 GLY B 86 GLN B 102 1 17 HELIX 21 21 LYS B 118 ASP B 132 1 15 HELIX 22 22 GLN B 144 ALA B 155 1 12 HELIX 23 23 GLN B 172 GLY B 183 1 12 HELIX 24 24 LEU B 192 GLN B 196 5 5 HELIX 25 25 ASN B 200 ASN B 211 1 12 HELIX 26 26 SER B 213 HIS B 225 1 13 HELIX 27 27 LYS B 235 ALA B 243 1 9 HELIX 28 28 SER B 251 ALA B 260 1 10 SHEET 1 A 2 THR A 8 LYS A 10 0 SHEET 2 A 2 GLU A 16 PRO A 18 -1 O MET A 17 N VAL A 9 SHEET 1 B 8 LEU A 22 GLY A 23 0 SHEET 2 B 8 SER A 47 ASP A 49 1 O ASP A 49 N LEU A 22 SHEET 3 B 8 PHE A 75 VAL A 80 1 O PHE A 75 N ILE A 48 SHEET 4 B 8 LEU A 106 ILE A 111 1 O LEU A 110 N VAL A 80 SHEET 5 B 8 ILE A 135 SER A 141 1 O ARG A 136 N LEU A 106 SHEET 6 B 8 VAL A 161 GLU A 165 1 O VAL A 161 N VAL A 140 SHEET 7 B 8 GLN A 185 TRP A 189 1 O GLU A 187 N VAL A 164 SHEET 8 B 8 VAL A 228 THR A 229 1 O VAL A 228 N ALA A 188 SHEET 1 C 2 THR B 8 LYS B 10 0 SHEET 2 C 2 GLU B 16 PRO B 18 -1 O MET B 17 N VAL B 9 SHEET 1 D 8 LEU B 22 GLY B 23 0 SHEET 2 D 8 SER B 47 ASP B 49 1 O ASP B 49 N LEU B 22 SHEET 3 D 8 PHE B 75 VAL B 80 1 O PHE B 75 N ILE B 48 SHEET 4 D 8 LEU B 106 ILE B 111 1 O LEU B 110 N VAL B 80 SHEET 5 D 8 ILE B 135 SER B 141 1 O ARG B 136 N LEU B 106 SHEET 6 D 8 VAL B 161 GLU B 165 1 O VAL B 161 N VAL B 140 SHEET 7 D 8 GLN B 185 TRP B 189 1 O GLU B 187 N VAL B 164 SHEET 8 D 8 VAL B 228 THR B 229 1 O VAL B 228 N ALA B 188 LINK O3 NO3 A 280 K K B 281 1555 1555 2.69 LINK O2 NO3 A 280 K K B 281 1555 1555 3.33 LINK O HOH A 486 K K B 282 1555 1555 2.96 LINK OD1 ASN B 82 K K B 281 1555 1555 3.01 LINK K K B 282 O HOH B 668 1555 1555 2.34 SITE 1 AC1 8 PHE A 25 SER A 190 PRO A 191 LEU A 192 SITE 2 AC1 8 MET A 193 GLN A 194 PRO A 231 LYS A 232 SITE 1 AC2 8 LEU A 192 GLY A 195 LEU A 198 ALA A 215 SITE 2 AC2 8 ARG A 238 HOH A 302 HOH A 329 HOH A 454 SITE 1 AC3 7 ASP A 117 LYS A 118 TYR A 119 LYS A 120 SITE 2 AC3 7 ASP A 121 HOH A 570 HOH A 666 SITE 1 AC4 10 TRP A 81 ASN A 82 LEU A 274 PHE A 276 SITE 2 AC4 10 HOH A 422 HOH A 599 HOH A 660 TRP B 81 SITE 3 AC4 10 LEU B 274 K B 281 SITE 1 AC5 5 ASP A 177 TYR A 178 GLY A 181 GLN A 182 SITE 2 AC5 5 HOH A 577 SITE 1 AC6 9 PHE B 25 SER B 190 PRO B 191 LEU B 192 SITE 2 AC6 9 MET B 193 GLN B 194 PRO B 231 LYS B 232 SITE 3 AC6 9 HOH B 508 SITE 1 AC7 10 LEU B 192 GLY B 195 LEU B 198 VAL B 214 SITE 2 AC7 10 ALA B 215 ARG B 238 HOH B 295 HOH B 301 SITE 3 AC7 10 HOH B 395 HOH B 467 SITE 1 AC8 6 ASP B 117 LYS B 118 TYR B 119 LYS B 120 SITE 2 AC8 6 ASP B 121 HOH B 658 SITE 1 AC9 8 LYS A 55 HOH A 356 ALA B 52 LYS B 55 SITE 2 AC9 8 ARG B 100 HOH B 307 HOH B 334 HOH B 421 SITE 1 BC1 3 NO3 A 280 TRP B 81 ASN B 82 SITE 1 BC2 2 HOH A 486 HOH B 668 CRYST1 79.656 123.075 57.239 90.00 90.00 90.00 P 21 21 2 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 0.012554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017471 0.00000