[English] 日本語
Yorodumi
- PDB-2mrm: Solution structure of the rhodanese domain of YgaP from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mrm
TitleSolution structure of the rhodanese domain of YgaP from E. coli
ComponentsMembrane protein
KeywordsMEMBRANE PROTEIN / rhodanese domain / YgaP / E. coli / Integral Membrane Protein
Function / homologyRhodanese-like domain / Oxidized Rhodanese; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsWang, W. / Zhou, P. / Tian, C. / Wu, F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Fast conformational exchange between the sulfur-free and persulfide-bound rhodanese domain of E. coli YgaP
Authors: Wang, W. / Zhou, P. / He, Y. / Yu, L. / Xiong, Y. / Tian, C. / Wu, F.
History
DepositionJul 12, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane protein


Theoretical massNumber of molelcules
Total (without water)12,6201
Polymers12,6201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Membrane protein / YgaP


Mass: 12620.390 Da / Num. of mol.: 1 / Fragment: UNP residues 1-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BU34_15760, CF57_07085, CF61_07785 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: W8T678

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HBHA(CO)NH
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
11123D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium chloride-1, 20 mM TRIS-2, 0.5 mM [U-100% 13C; U-100% 15N] YgaP-3, 90% H2O/10% D2O90% H2O/10% D2O
220 mM TRIS-4, 50 mM sodium chloride-5, 0.5 mM [U-100% 13C; U-100% 15N] YgaP-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloride-11
20 mMTRIS-21
0.5 mMYgaP-3[U-100% 13C; U-100% 15N]1
20 mMTRIS-42
50 mMsodium chloride-52
0.5 mMYgaP-6[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.05 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1875 / NOE intraresidue total count: 345 / NOE long range total count: 519 / NOE medium range total count: 459 / NOE sequential total count: 552 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

+
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