[English] 日本語
Yorodumi
- PDB-6idr: Crystal structure of Vibrio cholerae MATE transporter VcmN in the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6idr
TitleCrystal structure of Vibrio cholerae MATE transporter VcmN in the bent form
ComponentsMATE family efflux transporter
KeywordsTRANSPORT PROTEIN / MATE multidrug transporter
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.502 Å
AuthorsKusakizako, T. / Claxton, D.P. / Tanaka, Y. / Maturana, A.D. / Kuroda, T. / Ishitani, R. / Mchaourab, H.S. / Nureki, O.
CitationJournal: Structure / Year: 2019
Title: Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter.
Authors: Kusakizako, T. / Claxton, D.P. / Tanaka, Y. / Maturana, A.D. / Kuroda, T. / Ishitani, R. / Mchaourab, H.S. / Nureki, O.
History
DepositionSep 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MATE family efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9505
Polymers47,5241
Non-polymers1,4264
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19070 Å2
Unit cell
Length a, b, c (Å)52.254, 93.742, 100.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein MATE family efflux transporter / VcmN


Mass: 47523.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CGT79_05080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A1YWE9
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG 300, sodium citrate, ammonium fluoride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→93.74 Å / Num. obs: 17737 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.096 / Rrim(I) all: 0.252 / Net I/σ(I): 5.9 / Num. measured all: 118705 / Scaling rejects: 816
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.65.90.90619190.6350.4060.99598.5
9-93.7460.0464520.9970.020.0599.9

-
Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementResolution: 2.502→50.121 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 1766 10.03 %
Rwork0.2334 15840 -
obs0.2365 17606 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.71 Å2 / Biso mean: 34.9442 Å2 / Biso min: 12.48 Å2
Refinement stepCycle: final / Resolution: 2.502→50.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 35 34 3368
Biso mean--35.64 28.67 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033409
X-RAY DIFFRACTIONf_angle_d0.784638
X-RAY DIFFRACTIONf_chiral_restr0.023561
X-RAY DIFFRACTIONf_plane_restr0.005558
X-RAY DIFFRACTIONf_dihedral_angle_d12.4691170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5019-2.56960.30691350.279211851320
2.5696-2.64520.32171310.276111831314
2.6452-2.73060.32511260.273512111337
2.7306-2.82820.3011390.24712041343
2.8282-2.94140.23971380.223511871325
2.9414-3.07520.25911360.233712161352
3.0752-3.23730.33731320.23811941326
3.2373-3.44010.29391340.237712191353
3.4401-3.70570.27211370.223112131350
3.7057-4.07840.24311310.219712301361
4.0784-4.66820.24481340.238212321366
4.6682-5.880.2391450.229912411386
5.88-50.13150.22791480.204713251473

+
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