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- PDB-6fvn: DNA polymerase sliding clamp from Mycobacterium tuberculosis with... -

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Basic information

Entry
Database: PDB / ID: 6fvn
TitleDNA polymerase sliding clamp from Mycobacterium tuberculosis 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 / 3'-5' exonuclease activity / DNA replication / 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 speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.142 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,4078
Polymers171,4078
Non-polymers00
Water1,24369
1
A: Beta sliding clamp
J: P7 peptide
B: Beta sliding clamp
K: P7 peptide


Theoretical massNumber of molelcules
Total (without water)85,7034
Polymers85,7034
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-28 kcal/mol
Surface area31780 Å2
MethodPISA
2
C: Beta sliding clamp
H: P7 peptide
D: Beta sliding clamp
I: P7 peptide


Theoretical massNumber of molelcules
Total (without water)85,7034
Polymers85,7034
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-29 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.447, 126.761, 171.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 13:31 or (resid 32 and (name...
21(chain B and (resseq 13:31 or (resid 32 and (name...
31(chain C and (resseq 13:31 or (resid 32 and (name...
41(chain D and (resseq 13:20 or (resid 21 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 13:31 or (resid 32 and (name...A13 - 31
121(chain A and (resseq 13:31 or (resid 32 and (name...A32
131(chain A and (resseq 13:31 or (resid 32 and (name...A13 - 472
211(chain B and (resseq 13:31 or (resid 32 and (name...B13 - 31
221(chain B and (resseq 13:31 or (resid 32 and (name...B32
231(chain B and (resseq 13:31 or (resid 32 and (name...B12 - 472
311(chain C and (resseq 13:31 or (resid 32 and (name...C13 - 31
321(chain C and (resseq 13:31 or (resid 32 and (name...C32
331(chain C and (resseq 13:31 or (resid 32 and (name...C12 - 472
411(chain D and (resseq 13:20 or (resid 21 and (name...D13 - 20
421(chain D and (resseq 13:20 or (resid 21 and (name...D21
431(chain D and (resseq 13:20 or (resid 21 and (name...D12 - 472
441(chain D and (resseq 13:20 or (resid 21 and (name...D12 - 472
451(chain D and (resseq 13:20 or (resid 21 and (name...D12 - 472
461(chain D and (resseq 13:20 or (resid 21 and (name...D12 - 472

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Components

#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: 42150.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: dnaN, MT0002 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WNU0
#2: Protein/peptide
P7 peptide


Mass: 700.823 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 278 K / Method: vapor diffusion
Details: Acetate de Na 3.2M pH 6.9 18% PEG 3350 (1microliter)+ Hampton Research PEG Ion kit A2 (1microliter): 0.2M potassium fluoride, 20% PEG 3350 pH 7.3

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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: 3.142→101.837 Å / Num. obs: 27157 / % possible obs: 92.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 77.62 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.378 / Rpim(I) all: 0.107 / Rrim(I) all: 0.393 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.143-3.19812.43.1781.21530.3090.9353.31412.8
8.532-171.08512.20.04742.116870.9990.0140.04999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
MOLREPphasing
BUSTERrefinement
PHENIX1.10.1_2155refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TR7

4tr7


Resolution: 3.142→101.837 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.78
RfactorNum. reflection% reflection
Rfree0.2912 1351 4.98 %
Rwork0.2562 --
obs0.2579 27146 87.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.07 Å2 / Biso mean: 66.7222 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.142→101.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10607 0 0 69 10676
Biso mean---49.94 -
Num. residues----1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310791
X-RAY DIFFRACTIONf_angle_d0.8414782
X-RAY DIFFRACTIONf_chiral_restr0.0461865
X-RAY DIFFRACTIONf_plane_restr0.0041918
X-RAY DIFFRACTIONf_dihedral_angle_d11.6666413
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5566X-RAY DIFFRACTION10.71TORSIONAL
12B5566X-RAY DIFFRACTION10.71TORSIONAL
13C5566X-RAY DIFFRACTION10.71TORSIONAL
14D5566X-RAY DIFFRACTION10.71TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1422-3.25450.3546260.358748951517
3.2545-3.38480.3725950.31891914200967
3.3848-3.53880.33011320.2962744287695
3.5388-3.72540.32781580.297829153073100
3.7254-3.95880.3261530.28929033056100
3.9588-4.26450.31111530.258128843037100
4.2645-4.69370.26331660.222929303096100
4.6937-5.37280.25291530.227729223075100
5.3728-6.7690.28541560.273929793135100
6.769-101.89050.27531590.23131153274100

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