HEADER HYDROLASE 15-OCT-04 1VPB TITLE CRYSTAL STRUCTURE OF A PUTATIVE MODULATOR OF DNA GYRASE (BT3649) FROM TITLE 2 BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE MODULATOR OF DNA GYRASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: VPI-5482; SOURCE 5 GENE: BT3649; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PUTATIVE MODULATOR OF DNA GYRASE, STRUCTURAL GENOMICS, JOINT CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 22-MAY-24 1VPB 1 REMARK REVDAT 7 25-JAN-23 1VPB 1 REMARK SEQADV REVDAT 6 13-JUL-11 1VPB 1 VERSN REVDAT 5 28-JUL-10 1VPB 1 HEADER TITLE KEYWDS REVDAT 4 24-FEB-09 1VPB 1 VERSN REVDAT 3 03-OCT-06 1VPB 1 TITLE JRNL REVDAT 2 18-JAN-05 1VPB 1 REMARK REVDAT 1 09-NOV-04 1VPB 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE MODULATOR OF DNA GYRASE JRNL TITL 2 (BT3649) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.75 JRNL TITL 3 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 57756 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3091 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4159 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 252 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3329 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -1.06000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.635 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3555 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3199 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4820 ; 1.644 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7468 ; 0.832 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 471 ; 6.560 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;36.044 ;24.768 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 630 ;11.442 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;21.042 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 530 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4089 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 713 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 684 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3303 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1791 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2226 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 266 ; 0.139 ; 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): 14 ; 0.104 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 50 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.107 ; 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): 2336 ; 2.324 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 942 ; 0.593 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3636 ; 3.220 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1420 ; 5.427 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1184 ; 7.320 ;11.000 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 : 1 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 439 REMARK 3 ORIGIN FOR THE GROUP (A): 12.6584 20.6205 35.9151 REMARK 3 T TENSOR REMARK 3 T11: -0.1574 T22: -0.1988 REMARK 3 T33: -0.2017 T12: 0.0004 REMARK 3 T13: -0.0079 T23: -0.0163 REMARK 3 L TENSOR REMARK 3 L11: 0.3612 L22: 0.6376 REMARK 3 L33: 0.7103 L12: -0.1214 REMARK 3 L13: -0.0927 L23: -0.2372 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: 0.0806 S13: -0.1040 REMARK 3 S21: -0.1519 S22: -0.0737 S23: 0.0142 REMARK 3 S31: 0.2131 S32: 0.0184 S33: 0.0398 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 ELECTRON DENSITY FOR RESIDUES ALA42 AND LYS43 ARE POOR, REMARK 3 SO THESE TWO RESIDUES ARE NOT INCLUDED IN THE FINAL MODEL. REMARK 3 THE DATA USED IN THE FINAL REFINEMENT WAS FROM A NATIVE REMARK 3 CRYSTAL. THE REFINEMENT OF THE COORDINATES WAS RESTRAINED REMARK 3 WITH THE EXPERIMENTAL PHASES FROM A SELENOMETHIONINE MAD REMARK 3 EXPERIMENT FROM A SECOND CRYSTAL. REMARK 4 REMARK 4 1VPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000002034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-04; 18-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; ALS REMARK 200 BEAMLINE : BL11-1; 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979224; REMARK 200 1.020035,0.979718,0.979811 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(311) BENT REMARK 200 MONOCHROMATOR; DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : FLAT MIRROR; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61062 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.730 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.37 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DATA FROM A CRYSTAL OF SE-MET SUBSTITUTED REMARK 200 PROTEIN WAS USED FOR THE MAD PHASING EXPERIMENTS AND REMARK 200 DATA FROM A CRYSTAL OF NATIVE PROTEIN WAS USED FOR REMARK 200 THE FINAL REFINEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M KFORMATE, 20.0% PEG-3350, NO REMARK 280 BUFFER PH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, REMARK 280 TEMPERATURE 277K. 20.0% PEG-6000, 0.1M HEPES PH 7.0, VAPOR REMARK 280 DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 53.06000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.06000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.77050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 77.48400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.77050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 77.48400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.06000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.77050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 77.48400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.06000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.77050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 77.48400 REMARK 290 SMTRY3 8 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 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.06000 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 -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 ALA A 42 REMARK 465 LYS A 43 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 5 CD OE1 OE2 REMARK 470 LYS A 8 CD CE NZ REMARK 470 LYS A 19 CE NZ REMARK 470 GLU A 38 CD OE1 OE2 REMARK 470 MET A 44 CB CG SD CE REMARK 470 ARG A 46 CD NE CZ NH1 NH2 REMARK 470 GLN A 48 CG CD OE1 NE2 REMARK 470 GLU A 52 CD OE1 OE2 REMARK 470 ASN A 74 CG OD1 ND2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 GLU A 189 CD OE1 OE2 REMARK 470 ARG A 193 NE CZ NH1 NH2 REMARK 470 TYR A 197 CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 223 CZ NH1 NH2 REMARK 470 GLN A 231 CD OE1 NE2 REMARK 470 LYS A 390 CD CE NZ 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 102 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 105 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 183 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 246 NE - CZ - NH1 ANGL. DEV. = 3.3 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 THR A 333 -81.55 -119.22 REMARK 500 SER A 338 -55.31 -120.82 REMARK 500 THR A 392 -104.98 -119.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 441 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 356879 RELATED DB: TARGETDB DBREF 1VPB A 1 439 UNP Q8A1L2 Q8A1L2_BACTN 1 439 SEQADV 1VPB MET A -11 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB GLY A -10 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB SER A -9 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB ASP A -8 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB LYS A -7 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB ILE A -6 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB HIS A -5 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB HIS A -4 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB HIS A -3 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB HIS A -2 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB HIS A -1 UNP Q8A1L2 EXPRESSION TAG SEQADV 1VPB HIS A 0 UNP Q8A1L2 EXPRESSION TAG SEQRES 1 A 451 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 A 451 ILE THR ASP GLU ASN LYS LYS LEU ALA GLN TRP ALA MET SEQRES 3 A 451 ASP TYR ALA LEU LYS ASN GLY CYS GLN ALA ALA LYS VAL SEQRES 4 A 451 LEU LEU TYR SER SER SER ASN THR SER PHE GLU LEU ARG SEQRES 5 A 451 ASP ALA LYS MET ASP ARG LEU GLN GLN ALA SER GLU GLY SEQRES 6 A 451 GLY LEU SER LEU SER LEU TYR VAL ASP GLY ARG TYR GLY SEQRES 7 A 451 SER ILE SER THR ASN ARG LEU ASN ARG LYS GLU LEU GLU SEQRES 8 A 451 THR PHE ILE LYS ASN GLY ILE ASP SER THR ARG TYR LEU SEQRES 9 A 451 ALA LYS ASP GLU ALA ARG VAL LEU ALA ASP PRO SER ARG SEQRES 10 A 451 TYR TYR LYS GLY GLY LYS PRO ASP LEU LYS LEU TYR ASP SEQRES 11 A 451 ALA LYS PHE ALA SER LEU ASN PRO ASP ASP LYS ILE GLU SEQRES 12 A 451 MET ALA LYS ALA VAL ALA GLU GLU ALA LEU GLY LYS ASP SEQRES 13 A 451 GLU ARG ILE ILE SER VAL GLY SER SER TYR GLY ASP GLY SEQRES 14 A 451 GLU ASP PHE ALA TYR ARG LEU ILE SER ASN GLY PHE GLU SEQRES 15 A 451 GLY GLU THR LYS SER THR TRP TYR SER LEU SER ALA ASP SEQRES 16 A 451 ILE THR ILE ARG GLY GLU GLY GLU ALA ARG PRO SER ALA SEQRES 17 A 451 TYR TRP TYR GLU SER SER LEU TYR MET ASN ASP LEU ILE SEQRES 18 A 451 LYS LYS GLY ILE GLY GLN LYS ALA LEU GLU ARG VAL LEU SEQRES 19 A 451 ARG LYS LEU GLY GLN LYS LYS VAL GLN SER GLY LYS TYR SEQRES 20 A 451 THR MET VAL VAL ASP PRO MET ASN SER SER ARG LEU LEU SEQRES 21 A 451 SER PRO MET ILE SER ALA LEU ASN GLY SER ALA LEU GLN SEQRES 22 A 451 GLN LYS ASN SER PHE LEU LEU ASN LYS LEU ASN GLU LYS SEQRES 23 A 451 ILE ALA SER ASP ARG LEU THR LEU THR ASP GLU PRO HIS SEQRES 24 A 451 LEU VAL LYS ALA SER GLY ALA ARG TYR PHE ASP ASN GLU SEQRES 25 A 451 GLY ILE ALA THR GLU ARG ARG SER ILE PHE ASP LYS GLY SEQRES 26 A 451 VAL LEU ASN THR TYR PHE ILE ASP THR TYR ASN ALA LYS SEQRES 27 A 451 LYS MET GLY VAL ASP PRO THR ILE SER GLY SER SER ILE SEQRES 28 A 451 LEU VAL MET GLU THR GLY ASP LYS ASN LEU ASP GLY LEU SEQRES 29 A 451 ILE ALA GLY VAL GLU LYS GLY ILE LEU VAL THR GLY PHE SEQRES 30 A 451 ASN GLY GLY ASN ASN ASN SER SER THR GLY ASP PHE SER SEQRES 31 A 451 TYR GLY ILE GLU GLY PHE LEU ILE GLU ASN GLY LYS LEU SEQRES 32 A 451 THR GLN PRO VAL SER GLU MET ASN VAL THR GLY ASN LEU SEQRES 33 A 451 ILE THR LEU TRP ASN SER LEU VAL ALA THR GLY ASN ASP SEQRES 34 A 451 PRO ARG LEU ASN SER SER TRP ARG ILE PRO SER LEU VAL SEQRES 35 A 451 PHE GLU GLY VAL ASP PHE SER GLY LEU HET EDO A 440 4 HET EDO A 441 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 HOH *378(H2 O) HELIX 1 1 THR A 3 ASN A 20 1 18 HELIX 2 2 ASN A 74 ARG A 90 1 17 HELIX 3 3 ASP A 102 TYR A 106 5 5 HELIX 4 4 LYS A 120 LEU A 124 5 5 HELIX 5 5 ASN A 125 GLU A 139 1 15 HELIX 6 6 TYR A 204 LEU A 208 5 5 HELIX 7 7 GLY A 212 ARG A 223 1 12 HELIX 8 8 ASN A 243 ALA A 254 1 12 HELIX 9 9 ASN A 256 GLN A 262 1 7 HELIX 10 10 ASP A 321 GLY A 329 1 9 HELIX 11 11 ASN A 348 GLY A 355 1 8 HELIX 12 12 LEU A 404 SER A 410 1 7 SHEET 1 A 6 ARG A 64 THR A 70 0 SHEET 2 A 6 ARG A 46 VAL A 61 -1 N LEU A 55 O THR A 70 SHEET 3 A 6 ALA A 24 ARG A 40 -1 N SER A 36 O GLN A 48 SHEET 4 A 6 ILE A 147 ILE A 165 -1 O SER A 152 N LEU A 39 SHEET 5 A 6 PHE A 169 ILE A 186 -1 O ASP A 183 N GLY A 151 SHEET 6 A 6 SER A 195 SER A 202 -1 O ALA A 196 N ILE A 184 SHEET 1 B 7 LEU A 411 THR A 414 0 SHEET 2 B 7 LEU A 429 GLY A 438 -1 O VAL A 430 N VAL A 412 SHEET 3 B 7 LYS A 390 ASN A 403 -1 N ASN A 399 O SER A 437 SHEET 4 B 7 ASP A 376 GLU A 387 -1 N LEU A 385 O GLN A 393 SHEET 5 B 7 LYS A 358 ASN A 370 -1 N LEU A 361 O PHE A 384 SHEET 6 B 7 GLY A 233 VAL A 239 1 N VAL A 238 O VAL A 362 SHEET 7 B 7 LEU A 429 GLY A 438 -1 O PHE A 436 N GLY A 233 SHEET 1 C 5 VAL A 314 LEU A 315 0 SHEET 2 C 5 ARG A 307 ASP A 311 -1 N ASP A 311 O VAL A 314 SHEET 3 C 5 LEU A 282 ASP A 284 -1 N ASP A 284 O ARG A 307 SHEET 4 C 5 LEU A 340 MET A 342 -1 O VAL A 341 N THR A 283 SHEET 5 C 5 TRP A 424 ARG A 425 1 O ARG A 425 N LEU A 340 SITE 1 AC1 4 SER A 292 GLY A 293 ALA A 294 HOH A 604 SITE 1 AC2 7 LYS A 274 SER A 277 ASP A 278 LEU A 411 SITE 2 AC2 7 HOH A 483 HOH A 618 HOH A 731 CRYST1 73.541 154.968 106.120 90.00 90.00 90.00 C 2 2 21 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 0.013598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009423 0.00000