[English] 日本語
Yorodumi
- PDB-1fb6: CRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (OXID... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fb6
TitleCRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (OXIDIZED FORM)
ComponentsTHIOREDOXIN M
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


protein-disulfide reductase activity / enzyme activator activity / chloroplast / cytoplasm
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
Thioredoxin M-type, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCapitani, G. / Markovic-Housley, Z. / DelVal, G. / Morris, M. / Jansonius, J.N. / Schurmann, P.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of two functionally different thioredoxins in spinach chloroplasts.
Authors: Capitani, G. / Markovic-Housley, Z. / DelVal, G. / Morris, M. / Jansonius, J.N. / Schurmann, P.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOREDOXIN M
B: THIOREDOXIN M


Theoretical massNumber of molelcules
Total (without water)23,5872
Polymers23,5872
Non-polymers00
Water2,180121
1
A: THIOREDOXIN M


Theoretical massNumber of molelcules
Total (without water)11,7931
Polymers11,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIOREDOXIN M


Theoretical massNumber of molelcules
Total (without water)11,7931
Polymers11,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.71, 74.71, 74.00
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

-
Components

#1: Protein THIOREDOXIN M


Mass: 11793.436 Da / Num. of mol.: 2 / Fragment: OXIDIZED FORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Cellular location: CHLOROPLAST / Plasmid: PKK233-2 (MODIFIED) / Production host: Escherichia coli (E. coli) / References: UniProt: P07591
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium acetate, PEG monomethylether 2000, ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
250 mMTris-HCl1drop
30.02 %(w/v)1dropNaN3
40.2 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir
630 %(w/v)PEG2000 mme1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→29.6 Å / Num. obs: 14256 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.396 / % possible all: 92
Reflection shell
*PLUS
% possible obs: 92 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.1→29.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used overall anisotropic B-factor refinement and bulk solvent correction (X-PLOR 3.851 and CNS)
RfactorNum. reflection% reflectionSelection details
Rfree0.23 542 -RANDOM
Rwork0.204 ---
obs-14256 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 121 1765
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_improper_angle_d0.8
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 29.6 Å / σ(F): 0 / % reflection Rfree: 3.8 % / Rfactor obs: 0.204 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.8

+
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