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- PDB-6fvm: Mutant DNA polymerase sliding clamp from Escherichia coli with bo... -

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Basic information

Entry
Database: PDB / ID: 6fvm
TitleMutant DNA 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


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / 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 / : / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.631 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 1.1Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2Oct 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
H: P7 peptide
I: P7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,41015
Polymers83,1334
Non-polymers2,27711
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, details given in the primary citation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-40 kcal/mol
Surface area31770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.336, 78.653, 80.182
Angle α, β, γ (deg.)113.26, 97.82, 95.97
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABHI

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


Mass: 40865.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residue 346 is mutated from S in wild type to P in this mutant
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: dnaN, Z5192, ECs4636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A990
#2: Protein/peptide P7 peptide


Mass: 700.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 473 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: MES 50mM pH 6, CaCl2 50mM, PEG400 28%+ Hampton Research PEG Ion kit B3 (1 microliter): 0.2M lithium nitrate, 20% PEG 3350 pH 7.1

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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: 1.631→72.266 Å / Num. obs: 64980 / % possible obs: 87.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.631-1.6593.41.1911.1770.3080.7511.41831.6
4.426-72.2666.90.0354146880.9990.0140.03899.9

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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: 1.631→66.302 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 3141 4.84 %
Rwork0.1802 --
obs0.1821 64936 69.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.631→66.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 103 462 6279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086081
X-RAY DIFFRACTIONf_angle_d0.9668220
X-RAY DIFFRACTIONf_dihedral_angle_d17.5643762
X-RAY DIFFRACTIONf_chiral_restr0.058933
X-RAY DIFFRACTIONf_plane_restr0.0061075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6305-1.6560.14530.278559X-RAY DIFFRACTION1
1.656-1.68320.3608140.3205231X-RAY DIFFRACTION6
1.6832-1.71220.4119240.3167484X-RAY DIFFRACTION12
1.7122-1.74330.376470.3206916X-RAY DIFFRACTION23
1.7433-1.77680.3032680.29831328X-RAY DIFFRACTION33
1.7768-1.81310.3081010.28631817X-RAY DIFFRACTION44
1.8131-1.85250.29471140.27842312X-RAY DIFFRACTION58
1.8525-1.89560.3673720.27911542X-RAY DIFFRACTION37
1.8956-1.94310.2941650.25763121X-RAY DIFFRACTION78
1.9431-1.99560.32111350.24412948X-RAY DIFFRACTION72
1.9956-2.05430.28151860.21714035X-RAY DIFFRACTION99
2.0543-2.12060.25971990.21894040X-RAY DIFFRACTION99
2.1206-2.19640.2222010.19724007X-RAY DIFFRACTION100
2.1964-2.28440.26651420.19732606X-RAY DIFFRACTION63
2.2844-2.38830.23562150.18283964X-RAY DIFFRACTION100
2.3883-2.51430.23662040.18084059X-RAY DIFFRACTION100
2.5143-2.67180.22192120.17394079X-RAY DIFFRACTION100
2.6718-2.87810.20062040.17874065X-RAY DIFFRACTION100
2.8781-3.16770.20832100.16874052X-RAY DIFFRACTION100
3.1677-3.62610.20512020.15554029X-RAY DIFFRACTION100
3.6261-4.56830.17272150.13764048X-RAY DIFFRACTION100
4.5683-66.35720.20132080.17684053X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.7758 Å / Origin y: -15.2766 Å / Origin z: 12.1225 Å
111213212223313233
T0.045 Å20.0336 Å20.0281 Å2-0.1982 Å20.0389 Å2--0.1805 Å2
L-0.0628 °20.0723 °20.0404 °2-0.4506 °2-0.0145 °2--0.5239 °2
S0.009 Å °0.0302 Å °0.019 Å °-0.0084 Å °-0.0419 Å °0.0111 Å °-0.0034 Å °0.0184 Å °0.0341 Å °
Refinement TLS groupSelection details: all

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