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- PDB-3d1e: Crystal structure of E. coli sliding clamp (beta) bound to a poly... -

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Basic information

Entry
Database: PDB / ID: 3d1e
TitleCrystal structure of E. coli sliding clamp (beta) bound to a polymerase II peptide
Components
  • DNA polymerase III subunit beta
  • decamer from polymerase II C-terminal
KeywordsTRANSFERASE / TRANSCRIPTION / chemical probe / DNA polymerase / DNA sliding clamp / DNA replication / rational drug design / antibiotic target
Function / homology
Function and homology information


Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol
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 / : / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsGeorgescu, R.E. / Yurieva, O. / Seung-Sup, K. / Kuriyan, J. / Kong, X.-P. / O'Donnell, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp.
Authors: Georgescu, R.E. / Yurieva, O. / Kim, S.S. / Kuriyan, J. / Kong, X.P. / O'Donnell, M.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
P: decamer from polymerase II C-terminal


Theoretical massNumber of molelcules
Total (without water)82,3413
Polymers82,3413
Non-polymers00
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-8 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.139, 69.869, 73.119
Angle α, β, γ (deg.)112.890, 91.080, 99.280
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA polymerase III subunit beta / E.C.2.7.7.7


Mass: 40630.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaN / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A988, DNA-directed DNA polymerase
#2: Protein/peptide decamer from polymerase II C-terminal


Mass: 1080.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the sequence occurs naturally in E. coli
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.2
Details: 27.5% PEG400, 100 mM MES pH 6.2, 100 mM calcium chloride and 1% DMSO, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.959 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirror
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.959 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 68885 / Num. obs: 60707 / % possible obs: 94.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POL

2pol


Resolution: 1.9→33.55 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2646 4.7 %random
Rwork0.226 ---
obs-52670 92.9 %-
Solvent computationBsol: 59.9175 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.929 Å2
Baniso -1Baniso -2Baniso -3
1-6.61 Å27.85 Å2-2.78 Å2
2---1.53 Å2-1.4 Å2
3----5.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5733 0 0 472 6205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.253
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.9→2.02 Å /
Num. reflection% reflection
all7678 -
obs7678 84.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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