[English] 日本語
Yorodumi
- PDB-7mtl: Crystal structure of colibactin self-resistance protein ClbS in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mtl
TitleCrystal structure of colibactin self-resistance protein ClbS in complex with a dsDNA
Components
  • Colibactin self-protection protein ClbS
  • DNA (5'-D(*AP*AP*TP*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*GP*AP*AP*GP*TP*GP*GP*GP*AP*AP*TP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / hydrolase / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / DinB/YfiT-like putative metalloenzymes / DNA / DNA (> 10) / Colibactin self-protection protein ClbS
Function and homology information
Biological speciesEscherichia coli (E. coli)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.446 Å
AuthorsTripathi, P. / Bruner, S.D.
Citation
Journal: Biochemistry / Year: 2021
Title: Structural Basis for the Interactions of the Colibactin Resistance Gene Product ClbS with DNA.
Authors: Tripathi, P. / Bruner, S.D.
#1: Journal: Journal of American Chemical Society / Year: 2017
Title: ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance
Authors: Tripathi, P. / Bruner, S.D.
History
DepositionMay 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Colibactin self-protection protein ClbS
B: Colibactin self-protection protein ClbS
C: DNA (5'-D(*AP*AP*TP*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*AP*AP*GP*TP*GP*GP*GP*AP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)50,6734
Polymers50,6734
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.783, 75.878, 178.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Colibactin self-protection protein ClbS


Mass: 20747.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: clbS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, ...Gene: clbS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, EPS94_00180, EWK56_23755, FPI65_12320, FQU83_11985, GFU47_04510, GP945_05010, GP946_20500, HHG54_004716, HHJ44_00090, HJL93_000008, HJM41_001166, HJO44_004707, HJS53_002303, HmCmsJML146_00176, HNX34_25610, HV055_09710, HV098_09980, HV348_09415, NCTC9075_02752, NCTC9434_01964
Production host: Escherichia coli (E. coli) / References: UniProt: Q0P7K8
#2: DNA chain DNA (5'-D(*AP*AP*TP*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*AP*G)-3')


Mass: 4488.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*TP*GP*GP*AP*AP*GP*TP*GP*GP*GP*AP*AP*TP*T)-3')


Mass: 4689.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate pH 7.0, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.446→46.793 Å / Num. obs: 22255 / % possible obs: 99.86 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 11.79
Reflection shellResolution: 2.446→2.533 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2168 / CC1/2: 0.755 / % possible all: 98.77

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANR

6anr


Resolution: 2.446→46.793 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1173 5.28 %
Rwork0.2307 21050 -
obs0.2335 22223 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.75 Å2 / Biso mean: 64.8658 Å2 / Biso min: 29.3 Å2
Refinement stepCycle: final / Resolution: 2.446→46.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 609 0 10 3322
Biso mean---49.3 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.446-2.55710.37781170.3375256699
2.5571-2.69190.40481590.30542565100
2.6919-2.86050.36521400.30742610100
2.8605-3.08140.37561570.28912579100
3.0814-3.39140.30731450.24962601100
3.3914-3.88190.30321540.23292641100
3.8819-4.890.23671370.19662677100
4.89-46.7930.23171640.19352811100

+
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