HEADER TRANSFERASE/TRANSFERASE INHIBITOR 20-FEB-11 3QSB TITLE STRUCTURE OF E. COLI POLIIIBETA WITH (Z)-5-(1-((4'-FLUOROBIPHENYL-4- TITLE 2 YL)METHOXYIMINO)BUTYL)-2,2-DIMETHYL-4,6-DIOXOCYCLOHEXANECARBONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE III SUBUNIT BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA POLYMERASE III SUBUNIT BETA; COMPND 8 CHAIN: B; COMPND 9 EC: 2.7.7.7; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DNAN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: AN1459; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PND261; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 83333; SOURCE 14 STRAIN: K12; SOURCE 15 GENE: DNAN; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: AN1459; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PND261 KEYWDS DNA REPLICATION, SLIDING CLAMP, DNAN, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.WIJFFELS,W.M.JOHNSON,A.J.OAKLEY,K.TURNER,V.C.EPA,S.J.BRISCOE, AUTHOR 2 M.POLLEY,A.J.LIEPA,A.HOFMANN,J.BUCHARDT,C.CHRISTENSEN,P.PROSSELKOV, AUTHOR 3 B.P.DALRYMPLE,P.F.ALEWOOD,P.A.JENNINGS,N.E.DIXON,D.A.WINKLER REVDAT 5 06-DEC-23 3QSB 1 REMARK REVDAT 4 01-NOV-23 3QSB 1 REMARK LINK REVDAT 3 08-NOV-17 3QSB 1 REMARK REVDAT 2 05-MAR-14 3QSB 1 JRNL VERSN REVDAT 1 08-JUN-11 3QSB 0 JRNL AUTH G.WIJFFELS,W.M.JOHNSON,A.J.OAKLEY,K.TURNER,V.C.EPA, JRNL AUTH 2 S.J.BRISCOE,M.POLLEY,A.J.LIEPA,A.HOFMANN,J.BUCHARDT, JRNL AUTH 3 C.CHRISTENSEN,P.PROSSELKOV,B.P.DALRYMPLE,P.F.ALEWOOD, JRNL AUTH 4 P.A.JENNINGS,N.E.DIXON,D.A.WINKLER JRNL TITL BINDING INHIBITORS OF THE BACTERIAL SLIDING CLAMP BY DESIGN JRNL REF J.MED.CHEM. V. 54 4831 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21604761 JRNL DOI 10.1021/JM2004333 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 54957 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) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.317 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2902 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3493 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3310 REMARK 3 BIN FREE R VALUE SET COUNT : 172 REMARK 3 BIN FREE R VALUE : 0.3800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5686 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 365 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : 1.55000 REMARK 3 B33 (A**2) : -0.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 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): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.339 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6181 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8409 ; 2.205 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 794 ; 9.034 ; 5.025 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;39.206 ;23.741 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1100 ;20.726 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 60 ;20.834 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 935 ; 0.175 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4792 ; 0.010 ; 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): 3839 ; 1.233 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6246 ; 2.172 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2342 ; 3.424 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2163 ; 5.440 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3QSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000064040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57969 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.24300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1MMI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA MES PH 6.0, 50-60MM CACL2, REMARK 280 30%(V/V) PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K, PH 6.5 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 33.25950 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 B 334 CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 197 N 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 NH1 ARG A 205 O HOH A 512 2.00 REMARK 500 OD1 ASN B 118 O HOH B 391 2.03 REMARK 500 O HOH A 393 O HOH A 467 2.07 REMARK 500 O HOH B 391 O HOH B 483 2.07 REMARK 500 OE1 GLU B 303 O HOH B 509 2.08 REMARK 500 OE1 GLU B 140 O HOH B 436 2.08 REMARK 500 OE1 GLN A 91 O HOH A 382 2.08 REMARK 500 O ALA B 147 NH2 ARG B 197 2.11 REMARK 500 OD1 ASP A 77 NH2 ARG A 80 2.13 REMARK 500 O HOH B 393 O HOH B 531 2.18 REMARK 500 O VAL A 247 O HOH A 520 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 NE2 GLN A 123 O HOH B 526 1655 1.40 REMARK 500 OE1 GLN A 123 O HOH B 528 1655 1.88 REMARK 500 CD GLN A 123 O HOH B 526 1655 1.98 REMARK 500 O LYS A 250 O HOH B 485 1656 2.08 REMARK 500 OG SER A 109 OD2 ASP B 211 2655 2.10 REMARK 500 OE1 GLN A 123 O HOH B 526 1655 2.10 REMARK 500 O ASP A 39 O HOH B 445 1655 2.13 REMARK 500 OD1 ASP B 39 O HOH A 439 1455 2.16 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 ARG A 197 N ARG A 197 CA 0.515 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 LEU A 21 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 PRO A 25 C - N - CA ANGL. DEV. = 12.6 DEGREES REMARK 500 PRO A 25 C - N - CD ANGL. DEV. = -18.2 DEGREES REMARK 500 LEU A 98 CB - CG - CD1 ANGL. DEV. = 10.9 DEGREES REMARK 500 LEU A 138 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ASP A 173 CB - CG - OD1 ANGL. DEV. = -9.7 DEGREES REMARK 500 ASP A 173 CB - CG - OD2 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 176 CG - CD - NE ANGL. DEV. = -16.2 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 VAL A 179 CB - CA - C ANGL. DEV. = -18.9 DEGREES REMARK 500 LEU A 188 CA - CB - CG ANGL. DEV. = 18.7 DEGREES REMARK 500 ARG A 197 N - CA - CB ANGL. DEV. = 41.5 DEGREES REMARK 500 ARG A 197 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 LEU A 340 CA - CB - CG ANGL. DEV. = 14.7 DEGREES REMARK 500 LEU A 366 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 PRO B 20 C - N - CA ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG B 56 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU B 98 CB - CG - CD1 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG B 105 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 152 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 LEU B 188 CA - CB - CG ANGL. DEV. = 19.1 DEGREES REMARK 500 ARG B 205 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 205 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 245 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 245 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 279 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 279 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 LEU B 325 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 LYS B 332 N - CA - C ANGL. DEV. = -18.4 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 PRO A 20 -145.46 -56.76 REMARK 500 LEU A 21 123.02 75.05 REMARK 500 ARG A 24 36.87 26.42 REMARK 500 PRO A 25 26.46 2.27 REMARK 500 THR A 26 -27.74 42.87 REMARK 500 ASP A 39 -146.35 53.83 REMARK 500 ASP A 39 -121.14 56.71 REMARK 500 LEU A 49 -34.52 83.42 REMARK 500 HIS A 148 -68.45 -105.64 REMARK 500 PRO A 252 52.93 -98.52 REMARK 500 GLU A 298 5.67 -66.85 REMARK 500 PRO B 20 -96.47 -17.40 REMARK 500 LEU B 21 -2.47 -46.46 REMARK 500 THR B 26 -122.90 88.02 REMARK 500 LEU B 49 -40.16 89.35 REMARK 500 LEU B 130 146.50 -174.72 REMARK 500 ARG B 152 86.59 -67.49 REMARK 500 LYS B 250 -81.53 -44.90 REMARK 500 GLU B 298 5.94 -69.89 REMARK 500 TYR B 310 118.45 -162.61 REMARK 500 THR B 341 -64.99 -123.30 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 GLY A 23 ARG A 24 -144.72 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 743 A 367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 743 B 367 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MMI RELATED DB: PDB REMARK 900 SAME PROTEIN - WITHOUT LIGAND REMARK 900 RELATED ID: 2POL RELATED DB: PDB REMARK 900 FIRST DESCRIPTION OF THE PROTEIN STRUCTURE DBREF 3QSB A 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 3QSB B 1 366 UNP P0A988 DPO3B_ECOLI 1 366 SEQRES 1 A 366 MET LYS PHE THR VAL GLU ARG GLU HIS LEU LEU LYS PRO SEQRES 2 A 366 LEU GLN GLN VAL SER GLY PRO LEU GLY GLY ARG PRO THR SEQRES 3 A 366 LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN VAL ALA ASP SEQRES 4 A 366 GLY THR LEU SER LEU THR GLY THR ASP LEU GLU MET GLU SEQRES 5 A 366 MET VAL ALA ARG VAL ALA LEU VAL GLN PRO HIS GLU PRO SEQRES 6 A 366 GLY ALA THR THR VAL PRO ALA ARG LYS PHE PHE ASP ILE SEQRES 7 A 366 CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE ALA VAL GLN SEQRES 8 A 366 LEU GLU GLY GLU ARG MET LEU VAL ARG SER GLY ARG SER SEQRES 9 A 366 ARG PHE SER LEU SER THR LEU PRO ALA ALA ASP PHE PRO SEQRES 10 A 366 ASN LEU ASP ASP TRP GLN SER GLU VAL GLU PHE THR LEU SEQRES 11 A 366 PRO GLN ALA THR MET LYS ARG LEU ILE GLU ALA THR GLN SEQRES 12 A 366 PHE SER MET ALA HIS GLN ASP VAL ARG TYR TYR LEU ASN SEQRES 13 A 366 GLY MET LEU PHE GLU THR GLU GLY GLU GLU LEU ARG THR SEQRES 14 A 366 VAL ALA THR ASP GLY HIS ARG LEU ALA VAL CYS SER MET SEQRES 15 A 366 PRO ILE GLY GLN SER LEU PRO SER HIS SER VAL ILE VAL SEQRES 16 A 366 PRO ARG LYS GLY VAL ILE GLU LEU MET ARG MET LEU ASP SEQRES 17 A 366 GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE GLY SER ASN SEQRES 18 A 366 ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE PHE THR SER SEQRES 19 A 366 LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR ARG ARG VAL SEQRES 20 A 366 LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU ALA GLY CYS SEQRES 21 A 366 ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA ALA ILE LEU SEQRES 22 A 366 SER ASN GLU LYS PHE ARG GLY VAL ARG LEU TYR VAL SER SEQRES 23 A 366 GLU ASN GLN LEU LYS ILE THR ALA ASN ASN PRO GLU GLN SEQRES 24 A 366 GLU GLU ALA GLU GLU ILE LEU ASP VAL THR TYR SER GLY SEQRES 25 A 366 ALA GLU MET GLU ILE GLY PHE ASN VAL SER TYR VAL LEU SEQRES 26 A 366 ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN VAL ARG MET SEQRES 27 A 366 MET LEU THR ASP SER VAL SER SER VAL GLN ILE GLU ASP SEQRES 28 A 366 ALA ALA SER GLN SER ALA ALA TYR VAL VAL MET PRO MET SEQRES 29 A 366 ARG LEU SEQRES 1 B 366 MET LYS PHE THR VAL GLU ARG GLU HIS LEU LEU LYS PRO SEQRES 2 B 366 LEU GLN GLN VAL SER GLY PRO LEU GLY GLY ARG PRO THR SEQRES 3 B 366 LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN VAL ALA ASP SEQRES 4 B 366 GLY THR LEU SER LEU THR GLY THR ASP LEU GLU MET GLU SEQRES 5 B 366 MET VAL ALA ARG VAL ALA LEU VAL GLN PRO HIS GLU PRO SEQRES 6 B 366 GLY ALA THR THR VAL PRO ALA ARG LYS PHE PHE ASP ILE SEQRES 7 B 366 CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE ALA VAL GLN SEQRES 8 B 366 LEU GLU GLY GLU ARG MET LEU VAL ARG SER GLY ARG SER SEQRES 9 B 366 ARG PHE SER LEU SER THR LEU PRO ALA ALA ASP PHE PRO SEQRES 10 B 366 ASN LEU ASP ASP TRP GLN SER GLU VAL GLU PHE THR LEU SEQRES 11 B 366 PRO GLN ALA THR MET LYS ARG LEU ILE GLU ALA THR GLN SEQRES 12 B 366 PHE SER MET ALA HIS GLN ASP VAL ARG TYR TYR LEU ASN SEQRES 13 B 366 GLY MET LEU PHE GLU THR GLU GLY GLU GLU LEU ARG THR SEQRES 14 B 366 VAL ALA THR ASP GLY HIS ARG LEU ALA VAL CYS SER MET SEQRES 15 B 366 PRO ILE GLY GLN SER LEU PRO SER HIS SER VAL ILE VAL SEQRES 16 B 366 PRO ARG LYS GLY VAL ILE GLU LEU MET ARG MET LEU ASP SEQRES 17 B 366 GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE GLY SER ASN SEQRES 18 B 366 ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE PHE THR SER SEQRES 19 B 366 LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR ARG ARG VAL SEQRES 20 B 366 LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU ALA GLY CSO SEQRES 21 B 366 ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA ALA ILE LEU SEQRES 22 B 366 SER ASN GLU LYS PHE ARG GLY VAL ARG LEU TYR VAL SER SEQRES 23 B 366 GLU ASN GLN LEU LYS ILE THR ALA ASN ASN PRO GLU GLN SEQRES 24 B 366 GLU GLU ALA GLU GLU ILE LEU ASP VAL THR TYR SER GLY SEQRES 25 B 366 ALA GLU MET GLU ILE GLY PHE ASN VAL SER TYR VAL LEU SEQRES 26 B 366 ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN VAL ARG MET SEQRES 27 B 366 MET LEU THR ASP SER VAL SER SER VAL GLN ILE GLU ASP SEQRES 28 B 366 ALA ALA SER GLN SER ALA ALA TYR VAL VAL MET PRO MET SEQRES 29 B 366 ARG LEU MODRES 3QSB CSO B 260 CYS S-HYDROXYCYSTEINE HET CSO B 260 7 HET 743 A 367 32 HET 743 B 367 32 HETNAM CSO S-HYDROXYCYSTEINE HETNAM 743 (1R,5R)-5-{(1Z)-N-[(4'-FLUOROBIPHENYL-4-YL) HETNAM 2 743 METHOXY]BUTANIMIDOYL}-2,2-DIMETHYL-4,6- HETNAM 3 743 DIOXOCYCLOHEXANECARBONITRILE FORMUL 2 CSO C3 H7 N O3 S FORMUL 3 743 2(C26 H27 F N2 O3) FORMUL 5 HOH *365(H2 O) HELIX 1 1 ARG A 7 GLY A 19 1 13 HELIX 2 2 LEU A 27 LEU A 30 5 4 HELIX 3 3 ALA A 72 LEU A 82 1 11 HELIX 4 4 PRO A 112 PHE A 116 5 5 HELIX 5 5 PRO A 131 PHE A 144 1 14 HELIX 6 6 ARG A 152 ASN A 156 5 5 HELIX 7 7 PRO A 196 MET A 206 1 11 HELIX 8 8 ASP A 243 VAL A 247 5 5 HELIX 9 9 CYS A 260 ILE A 272 1 13 HELIX 10 10 VAL A 321 LYS A 332 1 12 HELIX 11 11 ARG B 7 SER B 18 1 12 HELIX 12 12 LEU B 27 LEU B 30 5 4 HELIX 13 13 ALA B 72 LEU B 82 1 11 HELIX 14 14 PRO B 112 PHE B 116 5 5 HELIX 15 15 PRO B 131 ALA B 141 1 11 HELIX 16 16 THR B 142 MET B 146 5 5 HELIX 17 17 ARG B 152 GLY B 157 5 6 HELIX 18 18 PRO B 196 MET B 206 1 11 HELIX 19 19 ASP B 243 LEU B 248 1 6 HELIX 20 20 CSO B 260 LEU B 273 1 14 HELIX 21 21 VAL B 321 LEU B 331 1 11 SHEET 1 A 8 LYS A 2 GLU A 6 0 SHEET 2 A 8 GLU A 87 GLU A 93 -1 O VAL A 90 N PHE A 3 SHEET 3 A 8 ARG A 96 SER A 101 -1 O ARG A 96 N GLU A 93 SHEET 4 A 8 SER A 104 SER A 109 -1 O PHE A 106 N VAL A 99 SHEET 5 A 8 GLU B 301 ASP B 307 -1 O GLU B 301 N SER A 107 SHEET 6 A 8 GLN B 289 ASN B 295 -1 N ILE B 292 O GLU B 304 SHEET 7 A 8 GLY B 280 SER B 286 -1 N SER B 286 O GLN B 289 SHEET 8 A 8 MET B 315 ASN B 320 -1 O ILE B 317 N LEU B 283 SHEET 1 B 8 GLY A 66 PRO A 71 0 SHEET 2 B 8 ASN A 32 ALA A 38 -1 N VAL A 37 O GLY A 66 SHEET 3 B 8 THR A 41 THR A 47 -1 O SER A 43 N GLN A 36 SHEET 4 B 8 MET A 51 ALA A 58 -1 O VAL A 57 N LEU A 42 SHEET 5 B 8 PHE A 230 LYS A 235 -1 O THR A 233 N GLU A 52 SHEET 6 B 8 ASN A 222 VAL A 227 -1 N ALA A 225 O PHE A 232 SHEET 7 B 8 LEU A 214 GLY A 219 -1 N GLY A 219 O ASN A 222 SHEET 8 B 8 SER A 124 LEU A 130 -1 N PHE A 128 O VAL A 216 SHEET 1 C 6 LYS A 254 GLY A 259 0 SHEET 2 C 6 ASN A 335 LEU A 340 -1 O LEU A 340 N LYS A 254 SHEET 3 C 6 VAL A 347 ASP A 351 -1 O GLN A 348 N MET A 339 SHEET 4 C 6 ALA A 357 VAL A 361 -1 O VAL A 361 N VAL A 347 SHEET 5 C 6 ARG A 176 VAL A 195 -1 N LEU A 177 O VAL A 360 SHEET 6 C 6 MET A 158 THR A 172 -1 O PHE A 160 N VAL A 193 SHEET 1 D 8 MET A 315 ASN A 320 0 SHEET 2 D 8 GLY A 280 SER A 286 -1 N LEU A 283 O ILE A 317 SHEET 3 D 8 GLN A 289 ASN A 295 -1 O LYS A 291 N TYR A 284 SHEET 4 D 8 GLU A 301 ASP A 307 -1 O LEU A 306 N LEU A 290 SHEET 5 D 8 SER B 104 SER B 109 -1 O SER B 107 N GLU A 301 SHEET 6 D 8 ARG B 96 SER B 101 -1 N VAL B 99 O PHE B 106 SHEET 7 D 8 GLU B 87 GLU B 93 -1 N GLU B 93 O ARG B 96 SHEET 8 D 8 LYS B 2 GLU B 6 -1 N PHE B 3 O VAL B 90 SHEET 1 E 8 GLY B 66 PRO B 71 0 SHEET 2 E 8 ASN B 32 ALA B 38 -1 N LEU B 33 O VAL B 70 SHEET 3 E 8 THR B 41 THR B 47 -1 O SER B 43 N GLN B 36 SHEET 4 E 8 MET B 51 ALA B 58 -1 O VAL B 57 N LEU B 42 SHEET 5 E 8 PHE B 230 LYS B 235 -1 O ILE B 231 N VAL B 54 SHEET 6 E 8 ASN B 222 VAL B 227 -1 N ALA B 225 O PHE B 232 SHEET 7 E 8 LEU B 214 ILE B 218 -1 N GLN B 217 O ARG B 224 SHEET 8 E 8 VAL B 126 LEU B 130 -1 N PHE B 128 O VAL B 216 SHEET 1 F 6 LYS B 254 GLY B 259 0 SHEET 2 F 6 ASN B 335 LEU B 340 -1 O MET B 338 N LEU B 256 SHEET 3 F 6 VAL B 347 ASP B 351 -1 O GLN B 348 N MET B 339 SHEET 4 F 6 ALA B 357 VAL B 361 -1 O VAL B 361 N VAL B 347 SHEET 5 F 6 ARG B 176 VAL B 195 -1 N LEU B 177 O VAL B 360 SHEET 6 F 6 MET B 158 THR B 172 -1 O GLY B 164 N LEU B 188 LINK C GLY B 259 N CSO B 260 1555 1555 1.32 LINK C CSO B 260 N ASP B 261 1555 1555 1.33 SITE 1 AC1 12 THR A 172 GLY A 174 ARG A 240 VAL A 247 SITE 2 AC1 12 SER A 346 VAL A 360 VAL A 361 MET A 362 SITE 3 AC1 12 HOH A 419 HOH A 423 HOH A 511 HOH A 513 SITE 1 AC2 8 THR B 172 GLY B 174 ARG B 246 VAL B 247 SITE 2 AC2 8 SER B 346 VAL B 360 VAL B 361 MET B 362 CRYST1 79.176 66.519 83.117 90.00 115.86 90.00 P 1 21 1 2 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 0.012630 0.000000 0.006121 0.00000 SCALE2 0.000000 0.015033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013370 0.00000