HEADER TRANSFERASE 28-OCT-08 3F1V TITLE E. COLI BETA SLIDING CLAMP, 148-153 ALA MUTANT CAVEAT 3F1V CHIRALITY ERROR AT CA CENTER OF ALA 149 CHAIN A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE III SUBUNIT BETA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DNAN, B3701, JW3678; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A-B5A KEYWDS PROTEIN, DNA REPLICATION, DNA-DIRECTED DNA POLYMERASE, KEYWDS 2 NUCLEOTIDYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CODY REVDAT 5 03-APR-24 3F1V 1 REMARK REVDAT 4 27-DEC-23 3F1V 1 REMARK REVDAT 3 20-OCT-21 3F1V 1 REMARK SEQADV LINK REVDAT 2 09-MAR-11 3F1V 1 REMARK REVDAT 1 01-SEP-09 3F1V 0 JRNL AUTH J.M.HELTZEL,S.K.SCOUTEN PONTICELLI,L.H.SANDERS,J.M.DUZEN, JRNL AUTH 2 V.CODY,J.PACE,E.H.SNELL,M.D.SUTTON JRNL TITL SLIDING CLAMP-DNA INTERACTIONS ARE REQUIRED FOR VIABILITY JRNL TITL 2 AND CONTRIBUTE TO DNA POLYMERASE MANAGEMENT IN ESCHERICHIA JRNL TITL 3 COLI. JRNL REF J.MOL.BIOL. V. 387 74 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19361435 JRNL DOI 10.1016/J.JMB.2009.01.050 REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 59193 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3133 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3318 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 183 REMARK 3 BIN FREE R VALUE : 0.4330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5648 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.02000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.01000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.809 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5744 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7780 ; 2.079 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 730 ; 6.864 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 256 ;38.767 ;24.062 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1008 ;17.807 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;17.131 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 894 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4336 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2592 ; 0.246 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3906 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 315 ; 0.183 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.265 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 125 ; 0.276 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.334 ; 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): 3797 ; 1.420 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5884 ; 2.127 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2187 ; 3.466 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1896 ; 5.410 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3F1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 28.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 FOR SHELL : 6.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 01K7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVIOR: 13% ISOPROPANOL, 100 MM REMARK 280 CACL2, 100 MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 CE MET A 1 O ALA A 67 0.97 REMARK 500 O HOH B 372 O HOH B 434 1.17 REMARK 500 CE MET A 1 C ALA A 67 2.08 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 420 O HOH B 573 1545 1.74 REMARK 500 O HOH B 376 O HOH B 555 1455 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 84 CB GLU A 84 CG 0.130 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 GLY A 19 N - CA - C ANGL. DEV. = 16.0 DEGREES REMARK 500 LEU A 44 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ALA A 67 CB - CA - C ANGL. DEV. = -11.7 DEGREES REMARK 500 ASN A 118 C - N - CA ANGL. DEV. = 15.7 DEGREES REMARK 500 ASN A 118 CB - CA - C ANGL. DEV. = -12.5 DEGREES REMARK 500 ASN A 118 N - CA - C ANGL. DEV. = 19.5 DEGREES REMARK 500 VAL A 227 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 LEU B 44 CB - CG - CD1 ANGL. DEV. = -15.2 DEGREES REMARK 500 ARG B 96 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU B 366 CA - CB - CG ANGL. DEV. = 14.6 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 74.77 27.88 REMARK 500 ARG A 24 22.50 137.70 REMARK 500 PRO A 25 114.82 -26.04 REMARK 500 ASP A 39 61.91 20.68 REMARK 500 LEU A 49 -33.14 84.14 REMARK 500 THR A 68 162.50 128.82 REMARK 500 ASN A 118 -76.14 -20.74 REMARK 500 ALA A 149 72.69 31.56 REMARK 500 ALA A 150 72.27 25.75 REMARK 500 TYR A 153 -125.40 -59.48 REMARK 500 ASN A 212 110.74 5.05 REMARK 500 ASN A 251 66.62 -152.62 REMARK 500 PHE A 278 78.58 -155.54 REMARK 500 THR A 341 -70.78 -119.42 REMARK 500 LEU B 49 -12.25 76.15 REMARK 500 ASN B 156 41.46 -85.41 REMARK 500 LYS B 254 97.76 -62.22 REMARK 500 THR B 341 -64.26 -122.57 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 ALA A 67 THR A 68 134.38 REMARK 500 ASN A 118 LEU A 119 -67.73 REMARK 500 ALA A 148 ALA A 149 119.18 REMARK 500 ALA A 150 ALA A 151 84.39 REMARK 500 ARG B 365 LEU B 366 148.95 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 CA A 367 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 118 O REMARK 620 2 LEU A 119 O 79.8 REMARK 620 3 HOH A 368 O 111.4 168.3 REMARK 620 4 HOH A 370 O 154.1 80.2 88.1 REMARK 620 5 HOH A 371 O 86.1 85.2 91.8 76.1 REMARK 620 6 HOH A 375 O 63.8 107.1 81.9 138.7 143.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 367 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 118 ND2 REMARK 620 2 LEU B 119 O 78.3 REMARK 620 3 HOH B 369 O 104.0 177.3 REMARK 620 4 HOH B 372 O 136.1 102.7 76.5 REMARK 620 5 HOH B 373 O 73.9 90.1 89.4 148.9 REMARK 620 6 HOH B 374 O 70.2 103.5 78.6 66.9 137.8 REMARK 620 7 HOH B 380 O 150.4 90.6 86.7 72.9 78.8 139.4 REMARK 620 8 HOH B 434 O 137.3 81.7 97.3 22.2 143.6 78.5 66.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 368 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OK7 RELATED DB: PDB DBREF 3F1V A 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 3F1V B 1 366 UNP P0A988 DPO3B_ECOLI 1 366 SEQADV 3F1V ALA A 148 UNP P0A988 HIS 148 ENGINEERED MUTATION SEQADV 3F1V ALA A 149 UNP P0A988 GLN 149 ENGINEERED MUTATION SEQADV 3F1V ALA A 150 UNP P0A988 ASP 150 ENGINEERED MUTATION SEQADV 3F1V ALA A 151 UNP P0A988 VAL 151 ENGINEERED MUTATION SEQADV 3F1V ALA A 152 UNP P0A988 ARG 152 ENGINEERED MUTATION SEQADV 3F1V ALA B 148 UNP P0A988 HIS 148 ENGINEERED MUTATION SEQADV 3F1V ALA B 149 UNP P0A988 GLN 149 ENGINEERED MUTATION SEQADV 3F1V ALA B 150 UNP P0A988 ASP 150 ENGINEERED MUTATION SEQADV 3F1V ALA B 151 UNP P0A988 VAL 151 ENGINEERED MUTATION SEQADV 3F1V ALA B 152 UNP P0A988 ARG 152 ENGINEERED MUTATION 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 ALA ALA ALA ALA ALA 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 ALA ALA ALA ALA ALA 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 CYS 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 HET CA A 367 1 HET CA B 367 1 HET CL B 368 1 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 3 CA 2(CA 2+) FORMUL 5 CL CL 1- FORMUL 6 HOH *378(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 GLN A 132 ALA A 141 1 10 HELIX 6 6 THR A 142 MET A 146 5 5 HELIX 7 7 ARG A 197 LEU A 207 1 11 HELIX 8 8 ASP A 243 LEU A 248 1 6 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 GLY B 19 1 13 HELIX 12 12 LEU B 27 LEU B 30 5 4 HELIX 13 13 ALA B 72 GLY B 81 1 10 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 ALA B 152 LEU B 155 5 4 HELIX 18 18 ARG B 197 MET B 206 1 10 HELIX 19 19 ASP B 243 VAL B 247 5 5 HELIX 20 20 CYS B 260 ILE B 272 1 13 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 ILE A 88 N VAL A 5 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 LEU A 108 N MET A 97 SHEET 5 A 8 GLU B 301 ASP B 307 -1 O GLU B 303 N ARG A 105 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 ARG B 282 O THR B 293 SHEET 8 A 8 MET B 315 ASN B 320 -1 O PHE B 319 N VAL B 281 SHEET 1 B 8 THR A 69 PRO A 71 0 SHEET 2 B 8 ASN A 32 ALA A 38 -1 N LEU A 33 O VAL A 70 SHEET 3 B 8 THR A 41 THR A 47 -1 O THR A 45 N LEU A 34 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 ILE A 231 N VAL A 54 SHEET 6 B 8 ASN A 222 VAL A 227 -1 N ALA A 225 O PHE A 232 SHEET 7 B 8 PRO A 213 ILE A 218 -1 N ARG A 215 O HIS A 226 SHEET 8 B 8 VAL A 126 PRO A 131 -1 N PHE A 128 O VAL A 216 SHEET 1 C 7 THR A 309 SER A 311 0 SHEET 2 C 7 LYS A 254 GLY A 259 -1 N GLU A 257 O THR A 309 SHEET 3 C 7 ASN A 335 LEU A 340 -1 O MET A 338 N LEU A 256 SHEET 4 C 7 VAL A 347 ASP A 351 -1 O GLU A 350 N ARG A 337 SHEET 5 C 7 ALA A 357 VAL A 361 -1 O VAL A 361 N VAL A 347 SHEET 6 C 7 ARG A 176 PRO A 196 -1 N LEU A 177 O VAL A 360 SHEET 7 C 7 GLY A 157 THR A 172 -1 O GLU A 165 N ILE A 184 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 THR A 293 N ARG A 282 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 ARG B 105 N GLU A 303 SHEET 6 D 8 ARG B 96 SER B 101 -1 N MET B 97 O LEU B 108 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 35 O THR B 68 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 LEU B 130 O LEU B 214 SHEET 1 F 7 THR B 309 TYR B 310 0 SHEET 2 F 7 LYS B 254 GLY B 259 -1 N GLU B 257 O THR B 309 SHEET 3 F 7 ASN B 335 LEU B 340 -1 O VAL B 336 N ALA B 258 SHEET 4 F 7 VAL B 347 ASP B 351 -1 O GLN B 348 N MET B 339 SHEET 5 F 7 ALA B 357 VAL B 361 -1 O TYR B 359 N ILE B 349 SHEET 6 F 7 ARG B 176 PRO B 196 -1 N LEU B 177 O VAL B 360 SHEET 7 F 7 GLY B 157 THR B 172 -1 O PHE B 160 N VAL B 193 LINK O ASN A 118 CA CA A 367 1555 1555 2.76 LINK O LEU A 119 CA CA A 367 1555 1555 2.24 LINK CA CA A 367 O HOH A 368 1555 1555 2.18 LINK CA CA A 367 O HOH A 370 1555 1555 2.33 LINK CA CA A 367 O HOH A 371 1555 1555 2.35 LINK CA CA A 367 O HOH A 375 1555 1555 2.57 LINK ND2 ASN B 118 CA CA B 367 1555 1555 2.28 LINK O LEU B 119 CA CA B 367 1555 1555 2.39 LINK CA CA B 367 O HOH B 369 1555 1555 2.37 LINK CA CA B 367 O HOH B 372 1555 1555 2.34 LINK CA CA B 367 O HOH B 373 1555 1555 2.30 LINK CA CA B 367 O HOH B 374 1555 1555 2.49 LINK CA CA B 367 O HOH B 380 1555 1555 2.56 LINK CA CA B 367 O HOH B 434 1555 1555 2.93 CISPEP 1 GLY A 19 PRO A 20 0 26.04 CISPEP 2 GLY A 22 GLY A 23 0 -3.74 SITE 1 AC1 6 ASN A 118 LEU A 119 HOH A 368 HOH A 370 SITE 2 AC1 6 HOH A 371 HOH A 375 SITE 1 AC2 8 ASN B 118 LEU B 119 HOH B 369 HOH B 372 SITE 2 AC2 8 HOH B 373 HOH B 374 HOH B 380 HOH B 434 SITE 1 AC3 3 GLU A 6 HOH A 405 HOH A 461 CRYST1 40.838 64.471 72.111 73.83 82.72 83.76 P 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 0.024487 -0.002678 -0.002501 0.00000 SCALE2 0.000000 0.015603 -0.004349 0.00000 SCALE3 0.000000 0.000000 0.014513 0.00000