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- PDB-6fvl: DNA polymerase sliding clamp from Escherichia coli with bound P7 ... -

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Basic information

Entry
Database: PDB / ID: 6fvl
TitleDNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
Components
  • Beta sliding clamp
  • P7 peptide
KeywordsDNA BINDING PROTEIN / DNA sliding clamp
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 / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation ...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 / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.975 Å
AuthorsMartiel, I. / Andre, C. / Olieric, V. / Guichard, G. / Burnouf, D.
Funding support France, 1items
OrganizationGrant numberCountry
IMMI2014013 France
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Peptide Interactions on Bacterial Sliding Clamps.
Authors: Andre, C. / Martiel, I. / Wolff, P. / Landolfo, M. / Lorber, B. / Silva da Veiga, C. / Dejaegere, A. / Dumas, P. / Guichard, G. / Olieric, V. / Wagner, J.G. / Burnouf, D.Y.
History
DepositionMar 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 17, 2024Group: 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
C: Beta sliding clamp
D: Beta sliding clamp
H: P7 peptide
I: P7 peptide
J: P7 peptide
K: P7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,92232
Polymers166,2268
Non-polymers4,69524
Water6,846380
1
A: Beta sliding clamp
B: Beta sliding clamp
H: P7 peptide
I: P7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,28721
Polymers83,1134
Non-polymers3,17417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-17 kcal/mol
Surface area32750 Å2
MethodPISA
2
C: Beta sliding clamp
D: Beta sliding clamp
J: P7 peptide
K: P7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,63511
Polymers83,1134
Non-polymers1,5227
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-23 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.900, 79.480, 85.317
Angle α, β, γ (deg.)65.83, 75.16, 75.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta sliding clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit


Mass: 40855.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: dnaN, b3701, JW3678 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A988
#2: Protein/peptide
P7 peptide


Mass: 700.823 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: MES 50mM pH 6, CaCl2 50mM PEG400 30% (1 microliter) + Hampton Research PEG Ion kit E6 (1 microliter): 0.2M sodium malonate pH6, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.975→57.055 Å / Num. obs: 76533 / % possible obs: 87.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 30.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
5.361-57.0553.50.03132.658080.9990.0270.03799.2
1.975-2.010.7061.11920.2340.6970.99325.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OK7

1ok7


Resolution: 1.975→57.055 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 3791 4.95 %
Rwork0.1888 --
obs0.191 76515 65.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.975→57.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11327 0 228 380 11935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711849
X-RAY DIFFRACTIONf_angle_d1.02615983
X-RAY DIFFRACTIONf_dihedral_angle_d15.2037293
X-RAY DIFFRACTIONf_chiral_restr0.0591833
X-RAY DIFFRACTIONf_plane_restr0.0072074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9755-2.00050.383260.2561125X-RAY DIFFRACTION3
2.0005-2.02680.3134150.2603221X-RAY DIFFRACTION5
2.0268-2.05460.255790.264355X-RAY DIFFRACTION9
2.0839-2.1150.2892330.2742761X-RAY DIFFRACTION20
2.115-2.14810.2649480.24671125X-RAY DIFFRACTION27
2.1481-2.18330.298800.23831351X-RAY DIFFRACTION33
2.1833-2.22090.30231020.23711676X-RAY DIFFRACTION41
2.2209-2.26130.3156870.24051440X-RAY DIFFRACTION35
2.2613-2.30480.26211540.23762571X-RAY DIFFRACTION63
2.3048-2.35190.28561680.24442983X-RAY DIFFRACTION73
2.3519-2.4030.28871910.23423490X-RAY DIFFRACTION85
2.403-2.45890.27381960.23093853X-RAY DIFFRACTION94
2.4589-2.52040.27332200.23374012X-RAY DIFFRACTION97
2.5204-2.58850.29041970.21634029X-RAY DIFFRACTION98
2.5885-2.66470.27421320.21312793X-RAY DIFFRACTION93
2.6647-2.75070.21211260.20272894X-RAY DIFFRACTION95
2.7507-2.8490.2662100.19164068X-RAY DIFFRACTION98
2.849-2.96310.24232190.19033991X-RAY DIFFRACTION98
2.9631-3.09790.2162430.19244032X-RAY DIFFRACTION98
3.0979-3.26130.23171990.18214068X-RAY DIFFRACTION98
3.2613-3.46560.22491760.18283334X-RAY DIFFRACTION80
3.4656-3.73310.21121740.17853658X-RAY DIFFRACTION89
3.7331-4.10870.20831690.16353671X-RAY DIFFRACTION89
4.1087-4.7030.20032170.14634073X-RAY DIFFRACTION99
4.703-5.92430.22742210.17854056X-RAY DIFFRACTION99
5.9243-57.07850.21071990.19394094X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.747 Å / Origin y: 54.4026 Å / Origin z: 9.2347 Å
111213212223313233
T0.2987 Å20.0212 Å2-0.0057 Å2-0.1568 Å2-0.0189 Å2--0.2357 Å2
L0.169 °20.0164 °20.0186 °2--0.0442 °20.0206 °2--0.0438 °2
S0.0088 Å °0.0123 Å °-0.0054 Å °-0.0194 Å °-0.0011 Å °-0.007 Å °-0.0185 Å °-0.0067 Å °-0.009 Å °
Refinement TLS groupSelection details: all

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