[English] 日本語
Yorodumi
- PDB-5y83: Crystal structure of YidC from Thermotoga maritima -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y83
TitleCrystal structure of YidC from Thermotoga maritima
ComponentsMembrane protein insertase YidCBiological membrane
KeywordsTRANSPORT PROTEIN / yidc / alb3 / oxa1 / sec
Function / homology
Function and homology information


membrane insertase activity / protein insertion into membrane / protein transport / plasma membrane
Similarity search - Function
: / Membrane insertase YidC / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18
Similarity search - Domain/homology
Membrane protein insertase YidC
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.842 Å
AuthorsHuang, Y. / Xin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China2013CB910603 China
CitationJournal: FASEB J. / Year: 2018
Title: Structure of YidC from Thermotoga maritima and its implications for YidC-mediated membrane protein insertion
Authors: Xin, Y. / Zhao, Y. / Zheng, J. / Zhou, H. / Zhang, X.C. / Tian, C. / Huang, Y.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 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: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)52,2621
Polymers52,2621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17050 Å2
Unit cell
Length a, b, c (Å)75.745, 103.600, 129.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Membrane protein insertase YidC / Biological membrane / Foldase YidC / Membrane integrase YidC / Membrane protein YidC


Mass: 52261.875 Da / Num. of mol.: 1 / Mutation: T24V, K25V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: yidC, TM_1461 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1H2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.87 Å3/Da / Density % sol: 81.04 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 20% PEG1500(w/v)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 10459 / % possible obs: 99.7 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Rrim(I) all: 0.128 / Χ2: 1.048 / Net I/σ(I): 4.4 / Num. measured all: 85442
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.8-3.948.310190.5390.940.926100
3.94-4.098.410160.720.6710.94100
4.09-4.288.410300.9350.3250.9531000.9020.961
4.28-4.58.310310.9690.181.0481000.4970.529
4.5-4.798.310410.990.1091.1241000.30.32
4.79-5.168.310320.990.1051.1041000.2910.31
5.16-5.678.210450.9820.11.0631000.2720.291
5.67-6.497.910560.9840.0781.0781000.2090.223
6.49-8.188.110710.9970.0361.1531000.10.106
8.18-507.511180.9970.0241.08997.10.0610.066

-
Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.842→42.758 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3124 729 5.16 %
Rwork0.2635 --
obs0.266 10459 75.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.72 Å2 / Biso mean: 69.7552 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 3.842→42.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 0 0 2679
Num. residues----342

+
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