[English] 日本語
Yorodumi
- PDB-2n4a: EC-NMR Structure of Ralstonia metallidurans Rmet_5065 Determined ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n4a
TitleEC-NMR Structure of Ralstonia metallidurans Rmet_5065 Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data. Northeast Structural Genomics Consortium target CrR115
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / AHSA1 / COG3832 / PF08327 / start domain / EC-NMR / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Activator of Hsp90 ATPase homologue 1-like C-terminal domain-containing protein
Function and homology information
Biological speciesCupriavidus metallidurans CH34 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsTang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Methods / Year: 2015
Title: Protein structure determination by combining sparse NMR data with evolutionary couplings.
Authors: Tang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D.S. / Montelione, G.T.
History
DepositionJun 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Remark 0THIS ENTRY 2N4A REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2LCG DETERMINED ...THIS ENTRY 2N4A REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2LCG DETERMINED BY AUTHORS: T.A.RAMELOT,Y.YANG,D.WANG,C.CICCOSANTI,H.JANJUA,R.NAIR,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE,M.A.KENNEDY,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,1371
Polymers16,1371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Uncharacterized protein


Mass: 16136.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans CH34 (bacteria)
Strain: CH34 / ATCC 43123 / DSM 2839 / Gene: Rmet_5065 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1LD49

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: Author used the CS, RDC and NOESY peak lists data from entry 2LCG.

-
Sample preparation

SampleConc.: 1.3 mM / Component: Rmet_5065-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]

-
Processing

NMR software
NameDeveloperClassification
RosettaBaker, D.refinement
EVfold-plmdata analysis
ASDPdata analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.data analysis
EC-NMRdata analysis
TALOS+data analysis
ReduceRichardson, J., Richardson, D.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Protons from the Rosetta models were removed and added back using Reduce.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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