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- PDB-6fvo: Mutant DNA polymerase sliding clamp from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 6fvo
TitleMutant DNA 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: 2.689 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

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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)171,52712
Polymers171,3678
Non-polymers1604
Water1,65792
1
A: Beta sliding clamp
B: Beta sliding clamp
H: P7 peptide
I: P7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7636
Polymers85,6834
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-57 kcal/mol
Surface area33980 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)85,7636
Polymers85,6834
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-37 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.488, 81.064, 90.015
Angle α, β, γ (deg.)68.640, 88.940, 62.560
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 10:20 or resseq 22:31 or (resid...
21(chain B and (resseq 10:20 or resseq 22:31 or (resid...
31(chain C and (resseq 10:20 or resseq 22:31 or (resid...
41(chain D and (resseq 10:20 or resseq 22:32 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 10:20 or resseq 22:31 or (resid...A10 - 20
121(chain A and (resseq 10:20 or resseq 22:31 or (resid...A22 - 31
131(chain A and (resseq 10:20 or resseq 22:31 or (resid...A32
211(chain B and (resseq 10:20 or resseq 22:31 or (resid...B10 - 20
221(chain B and (resseq 10:20 or resseq 22:31 or (resid...B22 - 31
231(chain B and (resseq 10:20 or resseq 22:31 or (resid...B0
241(chain B and (resseq 10:20 or resseq 22:31 or (resid...B8 - 400
251(chain B and (resseq 10:20 or resseq 22:31 or (resid...B8 - 400
261(chain B and (resseq 10:20 or resseq 22:31 or (resid...B8 - 400
271(chain B and (resseq 10:20 or resseq 22:31 or (resid...B8 - 400
281(chain B and (resseq 10:20 or resseq 22:31 or (resid...B8 - 400
311(chain C and (resseq 10:20 or resseq 22:31 or (resid...C10 - 20
321(chain C and (resseq 10:20 or resseq 22:31 or (resid...C22 - 31
331(chain C and (resseq 10:20 or resseq 22:31 or (resid...C32
341(chain C and (resseq 10:20 or resseq 22:31 or (resid...C8 - 401
351(chain C and (resseq 10:20 or resseq 22:31 or (resid...C8 - 401
361(chain C and (resseq 10:20 or resseq 22:31 or (resid...C8 - 401
371(chain C and (resseq 10:20 or resseq 22:31 or (resid...C8 - 401
411(chain D and (resseq 10:20 or resseq 22:32 or resseq...D10 - 20
421(chain D and (resseq 10:20 or resseq 22:32 or resseq...D22 - 32
431(chain D and (resseq 10:20 or resseq 22:32 or resseq...D0
441(chain D and (resseq 10:20 or resseq 22:32 or resseq...D51
451(chain D and (resseq 10:20 or resseq 22:32 or resseq...D51
461(chain D and (resseq 10:20 or resseq 22:32 or resseq...D8 - 401
471(chain D and (resseq 10:20 or resseq 22:32 or resseq...D8 - 401

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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: 42140.828 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Acetate de Na 3.2M pH 6.9 18% PEG 3350 (1microliter)+ Hampton Research PEG Ion kit B8 (1microliter): Magnesium formate dihydrate 0.2M; 20% PEG 3350; pH 7

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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: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionLowest resolution: 58.642 Å
Reflection shell

Num. unique obs: 1558 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.689-2.9953.60.8891.40.5770.5461.04649.1
8.531-68.5093.80.046220.9970.0280.05499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
STARANISOdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TR7

4tr7


Resolution: 2.689→58.642 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1575 5.06 %
Rwork0.2096 --
obs0.2122 31149 62.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.94 Å2 / Biso mean: 38.1844 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.689→58.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11263 0 4 92 11359
Biso mean--45.28 19.52 -
Num. residues----1557
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5527X-RAY DIFFRACTION15.498TORSIONAL
12B5527X-RAY DIFFRACTION15.498TORSIONAL
13C5527X-RAY DIFFRACTION15.498TORSIONAL
14D5527X-RAY DIFFRACTION15.498TORSIONAL

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