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- PDB-1ok7: A Conserved protein binding-site on Bacterial Sliding Clamps -

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Basic information

Entry
Database: PDB / ID: 1ok7
TitleA Conserved protein binding-site on Bacterial Sliding Clamps
Components
  • DNA POLYMERASE IIIDNA polymerase III holoenzyme
  • DNA POLYMERASE IV
KeywordsTRANSFERASE / DNA POLYMERASE IV / PEPTIDE INHIBITION / SLIDING CLAMP / TRANSLESION SYNTHESIS / DNA-DIRECTED DNA POLYMERASE / DNA REPLICATION
Function / homology
Function and homology information


Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / SOS response / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / error-free translesion synthesis ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / SOS response / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA synthesis involved in DNA repair / error-free translesion synthesis / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA damage response / magnesium ion binding / protein homodimerization activity / DNA binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
Beta sliding clamp / Beta sliding clamp / DNA polymerase IV
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBurnouf, D.Y. / Olieric, V. / Wagner, J. / Fujii, S. / Reinbolt, J. / Fuchs, R.P.P. / Dumas, P.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structural and Biochemical Analysis of Sliding Clamp/Ligand Interactions Suggest a Competition between Replicative and Translesion DNA Polymerases
Authors: Burnouf, D.Y. / Olieric, V. / Wagner, J. / Fujii, S. / Reinbolt, J. / Fuchs, R.P.P. / Dumas, P.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1992
Title: Three-Dimensional Structure of the Beta Subunit of Escherichia Coli DNA Polymerase III Holoenzyme: A Sliding DNA Clamp
Authors: Kong, X.-P. / Onrust, R. / O'Donnell, M. / Kuriyan, J.
History
DepositionJul 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Sep 16, 2015Group: Database references / Source and taxonomy / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE III
B: DNA POLYMERASE III
C: DNA POLYMERASE IV


Theoretical massNumber of molelcules
Total (without water)83,0873
Polymers83,0873
Non-polymers00
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-13.4 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 65.220, 73.380
Angle α, β, γ (deg.)73.11, 85.58, 85.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.18178, -0.82569, -0.53403), (-0.82476, -0.42376, 0.37444), (-0.53547, 0.37238, -0.75803)
Vector: -0.151, 0.075, 0.018)
DetailsPDB CONVENTION REQUIRES THAT THIS ENTRY BE CLASSIFIED AS TRIMERIC SINCE THE ASSEMBLY INCLUDES THREE CHAINS. HOWEVER CHAINS A AND B FORM A PHYSIOLOGICAL DIMER WHICH THEN INTERACTS WITH THE SMALLER CHAIN C.

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Components

#1: Protein DNA POLYMERASE III / DNA polymerase III holoenzyme / POLYMERASE / DNAN / B3701 / C4623 / Z5192 / ECS4636


Mass: 40630.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: DNAN GENE / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00583, UniProt: P0A988*PLUS, DNA-directed DNA polymerase
#2: Protein/peptide DNA POLYMERASE IV / / POL IV


Mass: 1826.185 Da / Num. of mol.: 1 / Fragment: C-TERMINUS OF DNA POL IV RESIDUES 336-351 / Source method: obtained synthetically / Details: C-TERMINUS (16 RESIDUES) OF DNA POL IV E.COLI / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: Q47155, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: N DEOXYNUCLEOSIDE TRIPHOSPHATE = N DIPHOSPHATE + {DNA}(N).
Sequence detailsDISORDERED LOOP (A19 - A26) WAS BUILT ONLY ON A STEREOCHEMICAL BASIS. ARG C10 WAS BUILT IN A RATHER ...DISORDERED LOOP (A19 - A26) WAS BUILT ONLY ON A STEREOCHEMICAL BASIS. ARG C10 WAS BUILT IN A RATHER POOR DENSITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 45 %
Crystal growpH: 6
Details: DROPS:0.92 ML OF PROTEIN AT 34.2 MG/ML, 1.89 ML OF P16 AT 1.1 MG/ML, 1 ML OF 2X RESERVOIR SOLUTION. RESERVOIR: 0.1 M MES PH 6.0, 0.1M CACL2 AND 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93922
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93922 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 85999 / % possible obs: 96.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.51
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 5.23 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2POL

2pol


Resolution: 1.65→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4225 5 %RANDOM
Rwork0.203 ---
obs0.203 84773 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.396 Å2 / ksol: 0.368559 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å2-2.04 Å2-2.73 Å2
2---2.48 Å20.52 Å2
3----1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5744 0 0 460 6204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.132
X-RAY DIFFRACTIONc_mcangle_it2.982.5
X-RAY DIFFRACTIONc_scbond_it3.492.5
X-RAY DIFFRACTIONc_scangle_it5.043
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 690 4.9 %
Rwork0.233 13271 -
obs--95.9 %

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