[English] 日本語
Yorodumi
- PDB-3grx: NMR STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN 3-GLUTATHIONE MIXE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3grx
TitleNMR STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN 3-GLUTATHIONE MIXED DISULFIDE COMPLEX, 20 STRUCTURES
ComponentsGLUTAREDOXIN 3
KeywordsELECTRON TRANSPORT / THIOL-DISULFIDE OXIDOREDUCTASE / THIOLTRANSFERASE / THIOREDOXIN SUPERFAMILY
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / glutathione binding / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm / cytosol
Similarity search - Function
Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutaredoxin 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNordstrand, K. / Aslund, F. / Holmgren, A. / Otting, G. / Berndt, K.D.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: NMR structure of Escherichia coli glutaredoxin 3-glutathione mixed disulfide complex: implications for the enzymatic mechanism.
Authors: Nordstrand, K. / slund, F. / Holmgren, A. / Otting, G. / Berndt, K.D.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Glutaredoxin-3 from Escherichia Coli. Amino Acid Sequence, 1H and 15N NMR Assignments, and Structural Analysis
Authors: Aslund, F. / Nordstrand, K. / Berndt, K.D. / Nikkola, M. / Bergman, T. / Ponstingl, H. / Jornvall, H. / Otting, G. / Holmgren, A.
History
DepositionAug 17, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Non-polymer description
Revision 1.4Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAREDOXIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3712
Polymers9,0631
Non-polymers3071
Water00
1


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

-
Components

#1: Protein GLUTAREDOXIN 3


Mass: 9063.272 Da / Num. of mol.: 1 / Mutation: C14S, C65Y
Source method: isolated from a genetically manipulated source
Details: COVALENT COMPLEX WITH GLUTATHIONE / Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 / Plasmid: PET-24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0AC62
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1213QF-COSY
131SMALL FLIP ANGLE COSY
141TOCSY
151NOESY
161OMEGA1-DECOUPLED NOESY
1712D HNHB
18115N-HSQC
191NOESY-15N-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING ONE SAMPLE OF RECOMBINANT GRX3[C14S/C65Y] AT NATURAL ABUNDANCE AND ONE SAMPLE OF UNIFORMLY 15N-LABELED GRX3[C14S/C65Y] COMPLEXED WITH UNLABELED GLUTATHIONE.

-
Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 0.05 M / pH: 6.0 / Pressure: 1 atm / Temperature: 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DMX 600 / Manufacturer: Bruker / Model: DMX 600 / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER, WUTHRICHrefinement
XEASYstructure solution
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE 20 CONFORMERS WERE ENERGY-MINIMIZED IN A 6 ANGSTROM SHELL OF EXPLICIT WATER.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / 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://pdbjlvh1.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