[English] 日本語
Yorodumi
- PDB-6fvm: Mutant DNA polymerase sliding clamp from Escherichia coli with bo... -

+
Open data


ID or keywords:

Loading...

-
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 / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
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 / :
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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 / Polyethylene glycol


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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more