[English] 日本語
Yorodumi
- PDB-5nii: Crystal structure of the atypical thioredoxin reductase TRi from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nii
TitleCrystal structure of the atypical thioredoxin reductase TRi from Desulfovibrio vulgaris Hildenborough
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase / Desulfovibrio / Anaerobes / Disulfide stress / NADPH motif
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase, putative
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsValette, O. / Tran, T.T.I. / Cavazza, C. / Caudeville, E. / Brasseur, G. / Dolla, A. / Talla, E. / Pieulle, L.
CitationJournal: Front Microbiol / Year: 2017
Title: Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris.
Authors: Valette, O. / Tran, T.T.T. / Cavazza, C. / Caudeville, E. / Brasseur, G. / Dolla, A. / Talla, E. / Pieulle, L.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,66015
Polymers65,3712
Non-polymers2,28813
Water5,729318
1
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,06111
Polymers32,6861
Non-polymers1,37510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5994
Polymers32,6861
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.387, 148.161, 152.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

CL

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase


Mass: 32685.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: DVU_1457 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72C27

-
Non-polymers , 5 types, 331 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3350, 100 mM BisTris pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→47.48 Å / Num. obs: 92563 / % possible obs: 99.2 % / Redundancy: 3.67 % / Net I/σ(I): 16.24

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FD8

3fd8


Resolution: 2→47.48 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2540 5 %RANDOM
Rwork0.1944 ---
obs0.1961 50800 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 147 318 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114648
X-RAY DIFFRACTIONf_angle_d1.2896301
X-RAY DIFFRACTIONf_dihedral_angle_d14.9271747
X-RAY DIFFRACTIONf_chiral_restr0.055701
X-RAY DIFFRACTIONf_plane_restr0.005821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.03840.33581340.32322530X-RAY DIFFRACTION95
2.0384-2.080.34661410.31062690X-RAY DIFFRACTION100
2.08-2.12520.3531390.28082632X-RAY DIFFRACTION99
2.1252-2.17470.33911410.27282674X-RAY DIFFRACTION99
2.1747-2.22910.32561390.25932636X-RAY DIFFRACTION99
2.2291-2.28930.2731410.23892676X-RAY DIFFRACTION99
2.2893-2.35670.26541410.23072681X-RAY DIFFRACTION100
2.3567-2.43280.30161420.22372695X-RAY DIFFRACTION100
2.4328-2.51970.27661390.21442652X-RAY DIFFRACTION100
2.5197-2.62060.25841410.21872677X-RAY DIFFRACTION100
2.6206-2.73980.26251410.21072680X-RAY DIFFRACTION99
2.7398-2.88430.26031420.20932698X-RAY DIFFRACTION100
2.8843-3.06490.22571420.20752686X-RAY DIFFRACTION100
3.0649-3.30150.22371420.19982706X-RAY DIFFRACTION99
3.3015-3.63370.22481400.18322660X-RAY DIFFRACTION98
3.6337-4.15920.19941440.15962739X-RAY DIFFRACTION99
4.1592-5.23910.19691430.15252716X-RAY DIFFRACTION98
5.2391-47.49350.17281480.17592832X-RAY DIFFRACTION98

+
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