[English] 日本語
Yorodumi
- PDB-1gh2: Crystal structure of the catalytic domain of a new human thioredo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gh2
TitleCrystal structure of the catalytic domain of a new human thioredoxin-like protein
ComponentsTHIOREDOXIN-LIKE PROTEIN
KeywordsELECTRON TRANSPORT / Redox-active center
Function / homology
Function and homology information


disulfide oxidoreductase activity / RHOBTB1 GTPase cycle / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / RHOV GTPase cycle / RHOU GTPase cycle / protein-disulfide reductase activity / RHOBTB2 GTPase cycle / proteasome complex ...disulfide oxidoreductase activity / RHOBTB1 GTPase cycle / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / RHOV GTPase cycle / RHOU GTPase cycle / protein-disulfide reductase activity / RHOBTB2 GTPase cycle / proteasome complex / nucleus / cytoplasm / cytosol
Similarity search - Function
PITH domain / PITH domain superfamily / PITH domain / PITH domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain / Galactose-binding-like domain superfamily / Glutaredoxin ...PITH domain / PITH domain superfamily / PITH domain / PITH domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain / Galactose-binding-like domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.22 Å
AuthorsJin, J. / Chen, X. / Guo, Q. / Yuan, J. / Qiang, B. / Rao, Z.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Crystal structure of the catalytic domain of a human thioredoxin-like protein.
Authors: Jin, J. / Chen, X. / Zhou, Y. / Bartlam, M. / Guo, Q. / Liu, Y. / Sun, Y. / Gao, Y. / Ye, S. / Li, G. / Rao, Z. / Qiang, B. / Yuan, J.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOREDOXIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,6281
Polymers11,6281
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.5, 48.5, 29.8
Angle α, β, γ (deg.)90, 99.59, 90
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein THIOREDOXIN-LIKE PROTEIN


Mass: 11628.187 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 - 108, CATALYTIC N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: FETAL BRAIN / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O43396
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5
Details: ammonium sulfate, pH 5.0, EVAPORATION, temperature 291.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Common name: ammonium sulfate

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→100 Å / Num. all: 6184 / Num. obs: 6170 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.4
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 6 % / Rmerge(I) obs: 0.316 / Num. unique all: 624 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 6710 / % possible obs: 99.8 %
Reflection shell
*PLUS
% possible obs: 98.7 % / Num. unique obs: 624

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.22→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.253 337 -
Rwork0.221 --
all-6026 -
obs-5689 92.3 %
Refinement stepCycle: LAST / Resolution: 2.22→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 44 860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_d1.975
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.97

+
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