HEADER TRANSFERASE 04-SEP-02 1MMI TITLE E. COLI DNA POLYMERASE BETA SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE III, BETA CHAIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DNAN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: AN1459; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PND261 KEYWDS DNA POLYMERASE BETA SUBUNIT, E. COLI, DNA REPLICATION, SLIDING CLAMP, KEYWDS 2 PROCESSIVITY FACTOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.J.OAKLEY,P.PROSSELKOV,G.WIJFFELS,J.L.BECK,M.C.J.WILCE,N.E.DIXON REVDAT 3 14-FEB-24 1MMI 1 REMARK REVDAT 2 24-FEB-09 1MMI 1 VERSN REVDAT 1 04-SEP-03 1MMI 0 JRNL AUTH A.J.OAKLEY,P.PROSSELKOV,G.WIJFFELS,J.L.BECK,M.C.WILCE, JRNL AUTH 2 N.E.DIXON JRNL TITL FLEXIBILITY REVEALED BY THE 1.85 A CRYSTAL STRUCTURE OF THE JRNL TITL 2 BETA SLIDING-CLAMP SUBUNIT OF ESCHERICHIA COLI DNA JRNL TITL 3 POLYMERASE III. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 1192 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12832762 JRNL DOI 10.1107/S0907444903009958 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 58907 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3119 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4099 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 231 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5688 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 665 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : 1.67000 REMARK 3 B33 (A**2) : -0.49000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.938 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5981 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5593 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8118 ; 1.370 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12992 ; 0.718 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 767 ; 8.103 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 1129 ;20.324 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 917 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6763 ; 0.022 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1194 ; 0.014 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1318 ; 0.260 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 7256 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 4097 ; 0.094 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 496 ; 0.253 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 21 ; 0.349 ; 0.500 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): 45 ; 0.297 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 124 ; 0.371 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 52 ; 0.344 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): 3 ; 0.605 ; 0.500 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): 3762 ; 2.545 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6103 ; 3.975 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2219 ; 6.380 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2015 ; 9.547 ; 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 1MMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017017. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : BENT GE(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62043 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 1.920 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.84 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.750 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 2POL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA/H MES, 50 TO 60 MM CACL2, REMARK 280 30% V/V PEG 400, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K 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 33.29750 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 300 REMARK: ASYMMETRIC UNIT CONTAINS PHYSIOLOGICALLY RELEVANT DIMER 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: 2620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 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 CZ ARG A 103 O HOH A 526 1.52 REMARK 500 NH2 ARG A 103 O HOH A 526 1.58 REMARK 500 NE2 GLN A 61 OE2 GLU A 87 1.87 REMARK 500 O ALA B 147 O HOH B 722 1.88 REMARK 500 O HOH B 441 O HOH B 659 1.90 REMARK 500 O HOH B 448 O HOH B 723 1.92 REMARK 500 O HOH B 588 O HOH B 710 1.97 REMARK 500 NH1 ARG A 137 O HOH A 519 1.99 REMARK 500 OD2 ASP A 173 O HOH A 459 1.99 REMARK 500 OD1 ASP A 77 NH2 ARG A 80 2.01 REMARK 500 O HOH A 527 O HOH A 666 2.01 REMARK 500 NE2 HIS B 148 O HOH B 549 2.04 REMARK 500 CD2 HIS B 148 O HOH B 549 2.05 REMARK 500 OD2 ASP A 261 O HOH A 656 2.06 REMARK 500 OD1 ASN B 118 O HOH B 399 2.09 REMARK 500 OE1 GLN A 186 O HOH A 538 2.09 REMARK 500 O ARG A 365 O HOH A 475 2.11 REMARK 500 NE ARG A 103 O HOH A 526 2.12 REMARK 500 O HOH B 552 O HOH B 639 2.14 REMARK 500 OD1 ASP A 229 O HOH A 614 2.14 REMARK 500 O HOH B 433 O HOH B 461 2.15 REMARK 500 O HOH B 603 O HOH B 641 2.15 REMARK 500 O HOH A 626 O HOH B 626 2.15 REMARK 500 NH2 ARG A 137 O HOH A 411 2.17 REMARK 500 NZ LYS A 235 O HOH A 578 2.17 REMARK 500 OG SER B 346 O HOH B 446 2.18 REMARK 500 OE2 GLU B 52 O HOH B 442 2.18 REMARK 500 NH1 ARG A 103 O HOH A 526 2.18 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 NE ARG A 215 OD1 ASP B 39 1455 1.82 REMARK 500 O HOH A 588 O HOH A 593 2757 1.92 REMARK 500 O HOH A 638 O HOH B 566 2746 2.04 REMARK 500 O HOH A 467 O HOH B 465 1556 2.04 REMARK 500 NE ARG A 215 OD2 ASP B 39 1455 2.14 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 ASP A 243 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 168 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP B 208 CB - CG - OD2 ANGL. DEV. = 5.6 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 LEU A 21 -168.03 -100.35 REMARK 500 PRO A 25 3.99 -65.44 REMARK 500 THR A 26 -70.43 52.88 REMARK 500 LEU A 27 97.89 -64.92 REMARK 500 ASP A 39 -144.69 65.72 REMARK 500 LEU A 49 -29.29 86.00 REMARK 500 GLN A 149 38.07 -143.67 REMARK 500 ASN A 156 43.58 -89.82 REMARK 500 ASN A 251 71.12 30.55 REMARK 500 THR A 341 -56.95 -129.95 REMARK 500 ASP A 342 -169.95 -168.12 REMARK 500 ARG B 24 59.79 -173.07 REMARK 500 LEU B 49 -19.63 82.49 REMARK 500 GLN B 149 57.81 -150.88 REMARK 500 ASN B 251 86.42 -153.10 REMARK 500 LYS B 332 68.78 -105.86 REMARK 500 THR B 341 -65.56 -123.19 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 24 130.71 REMARK 500 PRO A 25 THR A 26 -146.39 REMARK 500 MET B 364 ARG B 365 147.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 168 0.08 SIDE CHAIN REMARK 500 ARG B 56 0.08 SIDE CHAIN REMARK 500 ARG B 246 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 8 -11.38 REMARK 500 LEU A 98 -10.31 REMARK 500 GLY A 102 -11.21 REMARK 500 PRO A 242 -12.17 REMARK 500 LEU A 306 10.43 REMARK 500 LEU B 92 11.93 REMARK 500 PHE B 106 -11.80 REMARK 500 VAL B 151 -10.62 REMARK 500 ASN B 156 -10.30 REMARK 500 VAL B 227 -10.92 REMARK 500 LYS B 332 10.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2POL RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF THE BETA SUBUNIT OF ESCHERICHIA COLI REMARK 900 DNA POLYMERASE III HOLOENZYME: A SLIDING DNA CLAMP DBREF 1MMI A 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 1MMI 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 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 FORMUL 3 HOH *665(H2 O) HELIX 1 1 ARG A 7 SER A 18 1 12 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 152 LEU A 155 5 4 HELIX 8 8 ARG A 197 LEU A 207 1 11 HELIX 9 9 ASP A 243 VAL A 247 5 5 HELIX 10 10 CYS A 260 ILE A 272 1 13 HELIX 11 11 VAL A 321 LYS A 332 1 12 HELIX 12 12 ARG B 7 GLY B 19 1 13 HELIX 13 13 LEU B 27 LEU B 30 5 4 HELIX 14 14 ALA B 72 LEU B 82 1 11 HELIX 15 15 PRO B 112 PHE B 116 5 5 HELIX 16 16 PRO B 131 ALA B 141 1 11 HELIX 17 17 THR B 142 MET B 146 5 5 HELIX 18 18 ARG B 152 GLY B 157 5 6 HELIX 19 19 PRO B 196 MET B 206 1 11 HELIX 20 20 ASP B 243 LEU B 248 1 6 HELIX 21 21 CYS B 260 ILE B 272 1 13 HELIX 22 22 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 LEU A 98 N GLN A 91 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 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 TYR B 284 O LYS B 291 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 LEU A 33 O VAL A 70 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 ALA A 55 N LEU A 44 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 PRO A 213 ILE A 218 -1 N GLN A 217 O ARG A 224 SHEET 8 B 8 VAL A 126 PRO A 131 -1 N VAL A 126 O ILE A 218 SHEET 1 C 6 LYS A 254 GLY A 259 0 SHEET 2 C 6 ASN A 335 LEU A 340 -1 O VAL A 336 N ALA A 258 SHEET 3 C 6 VAL A 347 ASP A 351 -1 O GLN A 348 N MET A 339 SHEET 4 C 6 SER A 354 VAL A 361 -1 O VAL A 361 N VAL A 347 SHEET 5 C 6 LEU A 177 PRO A 196 -1 N VAL A 179 O ALA A 358 SHEET 6 C 6 GLY A 157 THR A 172 -1 O MET A 158 N VAL A 195 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 GLU A 304 N ILE A 292 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 SER B 101 O SER B 104 SHEET 7 D 8 GLU B 87 GLU B 93 -1 N GLN B 91 O LEU B 98 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 THR B 233 N GLU B 52 SHEET 6 E 8 ASN B 222 VAL B 227 -1 N VAL B 227 O PHE B 230 SHEET 7 E 8 LEU B 214 ILE B 218 -1 N ARG B 215 O HIS B 226 SHEET 8 E 8 VAL B 126 LEU B 130 -1 N PHE B 128 O VAL B 216 SHEET 1 F 8 HIS B 191 VAL B 195 0 SHEET 2 F 8 MET B 158 GLU B 163 -1 N PHE B 160 O VAL B 193 SHEET 3 F 8 GLU B 166 THR B 172 -1 O ARG B 168 N GLU B 161 SHEET 4 F 8 ARG B 176 PRO B 183 -1 O ALA B 178 N ALA B 171 SHEET 5 F 8 SER B 354 VAL B 361 -1 O VAL B 360 N LEU B 177 SHEET 6 F 8 VAL B 347 ASP B 351 -1 N ILE B 349 O TYR B 359 SHEET 7 F 8 ASN B 335 LEU B 340 -1 N ARG B 337 O GLU B 350 SHEET 8 F 8 LYS B 254 GLY B 259 -1 N ALA B 258 O VAL B 336 CRYST1 80.012 66.595 80.779 90.00 114.02 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012498 0.000000 0.005570 0.00000 SCALE2 0.000000 0.015016 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013553 0.00000