[English] 日本語
Yorodumi
- PDB-1thx: THIOREDOXIN-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1thx
TitleTHIOREDOXIN-2
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / OXIDO-REDUCTASE
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsSaarinen, M. / Gleason, F.K. / Eklund, H.
Citation
Journal: Structure / Year: 1995
Title: Crystal structure of thioredoxin-2 from Anabaena.
Authors: Saarinen, M. / Gleason, F.K. / Eklund, H.
#1: Journal: J.Bacteriol. / Year: 1992
Title: Activities of Two Dissimilar Thioredoxins from the Cyanobacterium Anabaena Sp. Pcc 7120
Authors: Gleason, F.K.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Isolation, Sequence, and Expression in Escherichia Coli of an Unusual Thioredoxin Gene from the Cyanobacterium Anabaena Sp. Strain Pcc 7120
Authors: Alam, J. / Curtis, S.E. / Gleason, F.K. / Gerami-Nejad, M. / Fuchs, J.A.
History
DepositionJul 7, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)12,8121
Polymers12,8121
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.480, 39.780, 60.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 76

-
Components

#1: Protein THIOREDOXIN / THIOREDOXIN 2


Mass: 12811.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: TRXA / Plasmid: PAN673.2 / Gene (production host): TRXA / Production host: Escherichia coli (E. coli) / References: UniProt: P20857
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.81 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220-25 %(w/w)PEG14501reservoircan be replaced with PEG-mono methyl ether 2000
3100 mMMES1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 22, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 10467 / % possible obs: 78.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.035
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 34 Å / Observed criterion σ(I): 13.9 / Num. measured all: 34399 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.64 Å / % possible obs: 49.5 %

-
Processing

Software
NameClassification
DENZO/CCP4data collection
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data reduction
X-PLORphasing
RefinementResolution: 1.6→7 Å / σ(F): 2
Details: RESIDUES SER 1 AND LYS 2 COULD BE BUILT IN TWO ALTERNATE ORIENTATIONS ROTATED 180 DEGREES AROUND THE C-ALPHA - C BOND OF LYS 2. MOST OF THESE ATOMS HAVE GOOD ELECTRON DENSITY IN BOTH ...Details: RESIDUES SER 1 AND LYS 2 COULD BE BUILT IN TWO ALTERNATE ORIENTATIONS ROTATED 180 DEGREES AROUND THE C-ALPHA - C BOND OF LYS 2. MOST OF THESE ATOMS HAVE GOOD ELECTRON DENSITY IN BOTH ORIENTATIONS, AND A POSITIVE DIFFERENCE FOURIER DENSITY SHOWS THE PRESENCE OF THE OTHER ORIENTATION, IN EITHER OF THE CASES.
RfactorNum. reflection
Rfree0.229 -
Rwork0.175 -
obs0.175 10103
Displacement parametersBiso mean: 18.41 Å2
Refinement stepCycle: LAST / Resolution: 1.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 74 918
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174 / Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3

+
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