[English] 日本語
Yorodumi
- PDB-2k4z: Solution NMR Structure of Allochromatium vinosum DsrR: Northeast ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2k4z
TitleSolution NMR Structure of Allochromatium vinosum DsrR: Northeast Structural Genomics Consortium Target OP5
ComponentsDsrR
Keywordsstructural genomics / unknown function / IscA/SufA/HesB like fold / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / METAL BINDING PROTEIN
Function / homologyHypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta / DsrR
Function and homology information
Biological speciesAllochromatium vinosum (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsCort, J.R. / Dahl, C. / Grimm, F. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the IscA-like Protein DsrR Involved in Sulfur Oxidation in Allochromatium vinosum
Authors: Dahl, C. / Cort, J.R. / Grimm, F.
History
DepositionJun 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DsrR


Theoretical massNumber of molelcules
Total (without water)13,7481
Polymers13,7481
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40fewest restraint violations, lowest energy, best geometry
RepresentativeModel #1close to the average, good geometry

-
Components

#1: Protein DsrR


Mass: 13748.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Species: vinosum / Gene: dsrR / Plasmid: pET15 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F299

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-13C HSQC
1232D 1H-13C HSQC
1333D CBCA(CO)NH
1433D HN(CA)CB
1533D (H)CCH-TOCSY
1633D HNCO
1733D C(CO)NH
1833D HBHA(CO)NH
1933D (H)CCH-COSY
11033D 1H-15N NOESY
11133D 1H-13C NOESY
11224D 1H-13C-13C-1H HMQC NOESY
11312D 1H-13C HSQC
11422D 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-10% 13C; U-100% 15N] DsrR, 93 % H2O, 7 % D2O, 50 mM Tris HCl, 500 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
21 mM [U-100% 13C; U-100% 15N] DsrR, 100 % D2O, 50 mM Tris HCl, 500 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
31 mM [U-100% 13C; U-100% 15N] DsrR, 93 % H2O, 7 % D2O, 50 mM Tris HCl, 500 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDsrR[U-10% 13C; U-100% 15N]1
93 %H2O1
7 %D2O1
50 mMTris HCl1
500 mMsodium chloride1
5 mMDTT1
0.02 %sodium azide1
1 mMDsrR[U-100% 13C; U-100% 15N]2
100 %D2O2
50 mMTris HCl2
500 mMsodium chloride2
5 mMDTT2
0.02 %sodium azide2
1 mMDsrR[U-100% 13C; U-100% 15N]3
93 %H2O3
7 %D2O3
50 mMTris HCl3
500 mMsodium chloride3
5 mMDTT3
0.02 %sodium azide3
Sample conditionsIonic strength: 625 / pH: 7.4 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

-
Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.data analysis
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1 / Details: final refinement done in explicit solvent
NMR representativeSelection criteria: close to the average, good geometry
NMR ensembleConformer selection criteria: fewest restraint violations, lowest energy, best geometry
Conformers calculated total number: 40 / 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