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- PDB-6e8e: Crystal structure of the Escherichia coli sliding clamp-MutL complex. -

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Basic information

Entry
Database: PDB / ID: 6e8e
TitleCrystal structure of the Escherichia coli sliding clamp-MutL complex.
Components(Beta sliding clamp,DNA mismatch repair protein MutL) x 2
KeywordsDNA BINDING PROTEIN / Complex
Function / homology
Function and homology information


mismatch repair complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / mismatched DNA binding / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / ATP-dependent DNA damage sensor activity / DNA strand elongation involved in DNA replication ...mismatch repair complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / mismatched DNA binding / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / ATP-dependent DNA damage sensor activity / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / mismatch repair / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site ...DNA mismatch repair protein, MutL / MutL, C-terminal domain, regulatory subdomain / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / 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 / : / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA mismatch repair protein MutL / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O139:H28 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGuarne, A. / Almawi, A.W.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Binding of the regulatory domain of MutL to the sliding beta-clamp is species specific.
Authors: Almawi, A.W. / Scotland, M.K. / Randall, J.R. / Liu, L. / Martin, H.K. / Sacre, L. / Shen, Y. / Pillon, M.C. / Simmons, L.A. / Sutton, M.D. / Guarne, A.
History
DepositionJul 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 7, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Oct 11, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sliding clamp,DNA mismatch repair protein MutL
B: Beta sliding clamp,DNA mismatch repair protein MutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,21513
Polymers114,1822
Non-polymers1,03311
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-76 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.390, 103.210, 141.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta sliding clamp,DNA mismatch repair protein MutL / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit


Mass: 57098.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: K12, E24377A / ETEC / Gene: dnaN, b3701, JW3678, mutL, EcE24377A_4728 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A988, UniProt: A7ZV39
#2: Protein Beta sliding clamp,DNA mismatch repair protein MutL / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit


Mass: 57082.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: K12, E24377A / ETEC / Gene: dnaN, b3701, JW3678, mutL, EcE24377A_4728 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A988, UniProt: A7ZV39
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100 mM Bis-Tris pH 5.5, 2 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.07→46.83 Å / Num. obs: 53370 / % possible obs: 97.5 % / Redundancy: 4.4 % / CC1/2: 0.998 / Net I/σ(I): 11.5
Reflection shellResolution: 2.25→2.32 Å / Num. unique all: 4976 / CC1/2: 0.356

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X9Z, 1PLQ

1x9z

1plq


Resolution: 2.25→46.83 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1586 2.97 %
Rwork0.19 --
obs0.191 53370 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6939 0 61 191 7191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047123
X-RAY DIFFRACTIONf_angle_d0.9599669
X-RAY DIFFRACTIONf_dihedral_angle_d15.8322610
X-RAY DIFFRACTIONf_chiral_restr0.0311137
X-RAY DIFFRACTIONf_plane_restr0.0031255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.32260.42391100.38013600X-RAY DIFFRACTION75
2.3226-2.40560.28321480.24434798X-RAY DIFFRACTION100
2.4056-2.50190.25831460.22444785X-RAY DIFFRACTION100
2.5019-2.61580.26421470.21784805X-RAY DIFFRACTION99
2.6158-2.75370.26761470.22074781X-RAY DIFFRACTION99
2.7537-2.92620.23111460.21094799X-RAY DIFFRACTION99
2.9262-3.15210.28111480.20594818X-RAY DIFFRACTION99
3.1521-3.46920.22361470.19574796X-RAY DIFFRACTION99
3.4692-3.9710.21731460.18044798X-RAY DIFFRACTION98
3.971-5.00210.16681490.14424846X-RAY DIFFRACTION98
5.0021-46.83970.21051520.17684958X-RAY DIFFRACTION96

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