HEADER TRANSFERASE 18-JUL-03 1OK7
TITLE A CONSERVED PROTEIN BINDING-SITE ON BACTERIAL SLIDING CLAMPS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE III;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: POLYMERASE, DNAN, B3701, C4623, Z5192, ECS4636;
COMPND 5 EC: 2.7.7.7;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: DNA POLYMERASE IV;
COMPND 9 CHAIN: C;
COMPND 10 FRAGMENT: C-TERMINUS OF DNA POL IV RESIDUES 336-351;
COMPND 11 SYNONYM: POL IV;
COMPND 12 EC: 2.7.7.7;
COMPND 13 ENGINEERED: YES;
COMPND 14 OTHER_DETAILS: C-TERMINUS (16 RESIDUES) OF DNA POL IV E.COLI
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B;
SOURCE 9 OTHER_DETAILS: DNAN GENE;
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 13 ORGANISM_TAXID: 562
KEYWDS TRANSFERASE, DNA POLYMERASE IV, PEPTIDE INHIBITION, SLIDING CLAMP,
KEYWDS 2 TRANSLESION SYNTHESIS, TRANSFERASE; DNA-DIRECTED DNA POLYMERASE, DNA
KEYWDS 3 REPLICATION
EXPDTA X-RAY DIFFRACTION
AUTHOR D.Y.BURNOUF,V.OLIERIC,J.WAGNER,S.FUJII,J.REINBOLT,R.P.P.FUCHS,P.DUMAS
REVDAT 5 13-DEC-23 1OK7 1 REMARK
REVDAT 4 16-SEP-15 1OK7 1 TITLE COMPND SOURCE KEYWDS
REVDAT 4 2 1 AUTHOR JRNL REMARK
REVDAT 3 13-FEB-13 1OK7 1 SOURCE REMARK VERSN FORMUL
REVDAT 2 24-FEB-09 1OK7 1 VERSN
REVDAT 1 15-JUL-04 1OK7 0
JRNL AUTH D.Y.BURNOUF,V.OLIERIC,J.WAGNER,S.FUJII,J.REINBOLT,
JRNL AUTH 2 R.P.P.FUCHS,P.DUMAS
JRNL TITL STRUCTURAL AND BIOCHEMICAL ANALYSIS OF SLIDING CLAMP/LIGAND
JRNL TITL 2 INTERACTIONS SUGGEST A COMPETITION BETWEEN REPLICATIVE AND
JRNL TITL 3 TRANSLESION DNA POLYMERASES
JRNL REF J.MOL.BIOL. V. 335 1187 2004
JRNL REFN ISSN 0022-2836
JRNL PMID 14729336
JRNL DOI 10.1016/J.JMB.2003.11.049
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH X.-P.KONG,R.ONRUST,M.O'DONNELL,J.KURIYAN
REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE BETA SUBUNIT OF
REMARK 1 TITL 2 ESCHERICHIA COLI DNA POLYMERASE III HOLOENZYME: A SLIDING
REMARK 1 TITL 3 DNA CLAMP
REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 69 425 1992
REMARK 1 REFN ISSN 0092-8674
REMARK 1 PMID 1349852
REMARK 1 DOI 10.1016/0092-8674(92)90445-I
REMARK 2
REMARK 2 RESOLUTION. 1.65 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8
REMARK 3 NUMBER OF REFLECTIONS : 84773
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 SET) : 0.203
REMARK 3 FREE R VALUE : 0.229
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 4225
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.90
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 13271
REMARK 3 BIN R VALUE (WORKING SET) : 0.2330
REMARK 3 BIN FREE R VALUE : 0.2840
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 690
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5744
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 460
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 19.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.90
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.67000
REMARK 3 B22 (A**2) : -2.48000
REMARK 3 B33 (A**2) : -1.19000
REMARK 3 B12 (A**2) : -2.04000
REMARK 3 B13 (A**2) : -2.73000
REMARK 3 B23 (A**2) : 0.52000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19
REMARK 3 ESD FROM SIGMAA (A) : 0.09
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.017
REMARK 3 BOND ANGLES (DEGREES) : 2.100
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80
REMARK 3 IMPROPER ANGLES (DEGREES) : 3.850
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 2.130 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.980 ; 2.500
REMARK 3 SIDE-CHAIN BOND (A**2) : 3.490 ; 2.500
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.040 ; 3.000
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.37
REMARK 3 BSOL : 48.40
REMARK 3
REMARK 3 NCS MODEL : UNRESTRAINED
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 PARAMETER FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1OK7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-03.
REMARK 100 THE DEPOSITION ID IS D_1290013075.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-APR-02
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 6.00
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.93922
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85999
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7
REMARK 200 DATA REDUNDANCY : 2.700
REMARK 200 R MERGE (I) : 0.05100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6
REMARK 200 DATA REDUNDANCY IN SHELL : 2.70
REMARK 200 R MERGE FOR SHELL (I) : 0.17800
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.230
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: PDB ENTRY 2POL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS:0.92 ML OF PROTEIN AT 34.2
REMARK 280 MG/ML, 1.89 ML OF P16 AT 1.1 MG/ML, 1 ML OF 2X RESERVOIR
REMARK 280 SOLUTION. RESERVOIR: 0.1 M MES PH 6.0, 0.1M CACL2 AND 30% PEG
REMARK 280 400, PH 6.00
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 300 REMARK: PDB CONVENTION REQUIRES THAT THIS ENTRY BE
REMARK 300 CLASSIFIED AS TRIMERIC SINCE THE ASSEMBLY INCLUDES
REMARK 300 THREE CHAINS. HOWEVER CHAINS A AND B FORM A
REMARK 300 PHYSIOLOGICAL DIMER WHICH THEN INTERACTS WITH THE
REMARK 300 SMALLER CHAIN C.
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 32970 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.4 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 400
REMARK 400 COMPOUND
REMARK 400 CATALYTIC ACTIVITY: N DEOXYNUCLEOSIDE TRIPHOSPHATE = N DIPHOSPHATE
REMARK 400 + {DNA}(N).
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 VAL C 1
REMARK 465 THR C 2
REMARK 465 LEU C 3
REMARK 465 LEU C 4
REMARK 465 ASP C 5
REMARK 465 PRO C 6
REMARK 465 GLN C 7
REMARK 465 MET C 8
REMARK 465 GLU C 9
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O ASP A 39 N GLY A 40 1.43
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 ASP A 39 C ASP A 39 O 0.960
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 39 CA - C - O ANGL. DEV. = -42.3 DEGREES
REMARK 500 ASP A 39 O - C - N ANGL. DEV. = -84.0 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 89.90 -56.61
REMARK 500 LEU A 21 177.54 175.52
REMARK 500 ARG A 24 74.54 24.51
REMARK 500 THR A 26 -113.02 -55.78
REMARK 500 ASP A 39 55.35 39.53
REMARK 500 LEU A 49 -25.71 84.48
REMARK 500 ASN A 156 49.99 -89.72
REMARK 500 PHE A 278 85.63 -155.78
REMARK 500 ASN A 288 28.76 49.85
REMARK 500 LYS A 332 51.93 31.10
REMARK 500 LEU B 49 -16.00 83.79
REMARK 500 THR B 341 -64.90 -123.19
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 ASP A 39 -179.67
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2018 DISTANCE = 6.72 ANGSTROMS
REMARK 525 HOH B2025 DISTANCE = 5.91 ANGSTROMS
REMARK 525 HOH B2031 DISTANCE = 6.50 ANGSTROMS
REMARK 525 HOH B2032 DISTANCE = 6.19 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1JQJ RELATED DB: PDB
REMARK 900 MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE DELTASUBUNIT WRENCH
REMARK 900 OF THE CLAMP LOADER COMPLEX OF E. COLI DNAPOLYMERASE III: STRUCTURE
REMARK 900 OF THE BETA-DELTA COMPLEX
REMARK 900 RELATED ID: 1JQL RELATED DB: PDB
REMARK 900 MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE DELTASUBUNIT WRENCH
REMARK 900 OF THE CLAMP LOADER COMPLEX OF E. COLI DNAPOLYMERASE III: STRUCTURE
REMARK 900 OF BETA-DELTA (1-140)
REMARK 900 RELATED ID: 2POL RELATED DB: PDB
REMARK 900 POL III (BETA SUBUNIT)
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 DISORDERED LOOP (A19 - A26) WAS BUILT ONLY ON A
REMARK 999 STEREOCHEMICAL BASIS. ARG C10 WAS BUILT IN A RATHER POOR
REMARK 999 DENSITY.
DBREF 1OK7 A 1 366 UNP P00583 DP3B_ECOLI 1 366
DBREF 1OK7 B 1 366 UNP P00583 DP3B_ECOLI 1 366
DBREF 1OK7 C 1 16 UNP Q47155 DPO4_ECOLI 336 351
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
SEQRES 1 C 16 VAL THR LEU LEU ASP PRO GLN MET GLU ARG GLN LEU VAL
SEQRES 2 C 16 LEU GLY LEU
FORMUL 4 HOH *460(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 GLN A 143 1 12
HELIX 6 6 PHE A 144 MET A 146 5 3
HELIX 7 7 ARG A 152 LEU A 155 5 4
HELIX 8 8 ARG A 197 MET A 206 1 10
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 SER B 18 1 12
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 AA 8 LYS A 2 GLU A 6 0
SHEET 2 AA 8 GLU A 87 GLU A 93 -1 O ILE A 88 N VAL A 5
SHEET 3 AA 8 ARG A 96 SER A 101 -1 O ARG A 96 N GLU A 93
SHEET 4 AA 8 SER A 104 SER A 109 -1 O SER A 104 N SER A 101
SHEET 5 AA 8 GLU B 301 ASP B 307 -1 O GLU B 301 N SER A 107
SHEET 6 AA 8 GLN B 289 ASN B 295 -1 O LEU B 290 N LEU B 306
SHEET 7 AA 8 GLY B 280 SER B 286 -1 O ARG B 282 N THR B 293
SHEET 8 AA 8 MET B 315 ASN B 320 -1 O MET B 315 N VAL B 285
SHEET 1 AB 8 GLY A 66 PRO A 71 0
SHEET 2 AB 8 ASN A 32 ALA A 38 -1 O LEU A 33 N VAL A 70
SHEET 3 AB 8 THR A 41 THR A 47 -1 O THR A 41 N ALA A 38
SHEET 4 AB 8 MET A 51 ALA A 58 -1 O MET A 53 N GLY A 46
SHEET 5 AB 8 PHE A 230 LYS A 235 -1 O ILE A 231 N VAL A 54
SHEET 6 AB 8 ASN A 222 VAL A 227 -1 O ILE A 223 N SER A 234
SHEET 7 AB 8 PRO A 213 GLY A 219 -1 O ARG A 215 N HIS A 226
SHEET 8 AB 8 SER A 124 PRO A 131 -1 N GLU A 125 O ILE A 218
SHEET 1 AC 6 GLY A 157 THR A 172 0
SHEET 2 AC 6 ARG A 176 PRO A 196 -1 O ALA A 178 N ALA A 171
SHEET 3 AC 6 SER A 354 VAL A 361 -1 O SER A 356 N SER A 181
SHEET 4 AC 6 VAL A 347 ASP A 351 -1 O VAL A 347 N VAL A 361
SHEET 5 AC 6 ASN A 335 LEU A 340 -1 O ARG A 337 N GLU A 350
SHEET 6 AC 6 LYS A 254 GLY A 259 -1 O LYS A 254 N LEU A 340
SHEET 1 AD 8 MET A 315 ASN A 320 0
SHEET 2 AD 8 GLY A 280 SER A 286 -1 O VAL A 281 N PHE A 319
SHEET 3 AD 8 GLN A 289 ASN A 295 -1 O GLN A 289 N SER A 286
SHEET 4 AD 8 GLU A 301 ASP A 307 -1 O ALA A 302 N ALA A 294
SHEET 5 AD 8 SER B 104 SER B 109 -1 O ARG B 105 N GLU A 303
SHEET 6 AD 8 ARG B 96 SER B 101 -1 O MET B 97 N LEU B 108
SHEET 7 AD 8 GLU B 87 GLU B 93 -1 O ALA B 89 N ARG B 100
SHEET 8 AD 8 LYS B 2 GLU B 6 -1 O PHE B 3 N VAL B 90
SHEET 1 BA 8 GLY B 66 PRO B 71 0
SHEET 2 BA 8 ASN B 32 ALA B 38 -1 O LEU B 33 N VAL B 70
SHEET 3 BA 8 THR B 41 THR B 47 -1 O THR B 41 N ALA B 38
SHEET 4 BA 8 MET B 51 ALA B 58 -1 O MET B 53 N GLY B 46
SHEET 5 BA 8 PHE B 230 LYS B 235 -1 O ILE B 231 N VAL B 54
SHEET 6 BA 8 ASN B 222 VAL B 227 -1 O ILE B 223 N SER B 234
SHEET 7 BA 8 LEU B 214 ILE B 218 -1 O ARG B 215 N HIS B 226
SHEET 8 BA 8 VAL B 126 LEU B 130 -1 O VAL B 126 N ILE B 218
SHEET 1 BB 6 MET B 158 THR B 172 0
SHEET 2 BB 6 ARG B 176 VAL B 195 -1 O ALA B 178 N ALA B 171
SHEET 3 BB 6 SER B 354 VAL B 361 -1 O SER B 356 N SER B 181
SHEET 4 BB 6 VAL B 347 ASP B 351 -1 O VAL B 347 N VAL B 361
SHEET 5 BB 6 ASN B 335 LEU B 340 -1 O ARG B 337 N GLU B 350
SHEET 6 BB 6 LYS B 254 GLY B 259 -1 O LYS B 254 N LEU B 340
CRYST1 41.230 65.220 73.380 73.11 85.58 85.80 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 0.024254 -0.001781 -0.001424 0.00000
SCALE2 0.000000 0.015374 -0.004597 0.00000
SCALE3 0.000000 0.000000 0.014266 0.00000
MTRIX1 1 0.181780 -0.825690 -0.534030 -0.15100 1
MTRIX2 1 -0.824760 -0.423760 0.374440 0.07500 1
MTRIX3 1 -0.535470 0.372380 -0.758030 0.01800 1