[English] 日本語
Yorodumi
- PDB-1vdc: STRUCTURE OF NADPH DEPENDENT THIOREDOXIN REDUCTASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vdc
TitleSTRUCTURE OF NADPH DEPENDENT THIOREDOXIN REDUCTASE
ComponentsNADPH DEPENDENT THIOREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / HYPOTHETICAL PROTEIN / REDOX-ACTIVE CENTER / DISULFIDE OXIDOREDUCTASE / THIOREDOXIN REDUCTASE / FLAVIN ADENINE DINULEOTIDE
Function / homology
Function and homology information


thioredoxin-disulfide reductase / chloroplast envelope / thioredoxin-disulfide reductase (NADPH) activity / positive regulation of cell division / removal of superoxide radicals / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / 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 1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDai, S. / Eklund, H.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of Arabidopsis thaliana NADPH dependent thioredoxin reductase at 2.5 A resolution.
Authors: Dai, S. / Saarinen, M. / Ramaswamy, S. / Meyer, Y. / Jacquot, J.P. / Eklund, H.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of Escherichia Coli Thioredoxin Reductase Refined at 2 A Resolution. Implications for a Large Conformational Change During Catalysis
Authors: Waksman, G. / Krishna, T.S. / Williams Junior, C.H. / Kuriyan, J.
History
DepositionSep 22, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH DEPENDENT THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3023
Polymers35,4201
Non-polymers8822
Water5,873326
1
A: NADPH DEPENDENT THIOREDOXIN REDUCTASE
hetero molecules

A: NADPH DEPENDENT THIOREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6036
Polymers70,8402
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7950 Å2
ΔGint-60 kcal/mol
Surface area25540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.974, 89.974, 175.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein NADPH DEPENDENT THIOREDOXIN REDUCTASE / NTR


Mass: 35420.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: PET / Gene: ATTHIREDB / Plasmid: PET-3D / Gene (production host): ATTHIREDB / Production host: Escherichia coli (E. coli) / References: UniProt: Q39243, EC: 1.6.4.5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNADPH CAN ALSO BE SEEN WITH LOW OCCUPANCY BUT NO COORDINATES ARE GIVEN FOR IT IN THIS ENTRY.
Sequence detailsPROTEIN SEQUENCE NUMBERING IS BASED ON E. COLI NTR SEQUENCE AND IS NOT THE SAME AS THE SEQUENCE ...PROTEIN SEQUENCE NUMBERING IS BASED ON E. COLI NTR SEQUENCE AND IS NOT THE SAME AS THE SEQUENCE NUMBERING IN GENBANK.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.05 Å3/Da / Density % sol: 70.6 %
Crystal growDetails: 7% ISOPROPANOL (OR 4% MPD) AND 1.8 M AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 %(v/v)isopropanol1reservoiror 4 % MPD
21.8 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 175 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.857
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.857 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 25745 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.81 % / Biso Wilson estimate: 30.92 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.487 / % possible all: 100
Reflection
*PLUS
Num. obs: 20556 / Num. measured all: 139995
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRB

1trb


Resolution: 2.5→20 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.243 2455 10 %
Rwork0.188 --
obs0.188 24816 100 %
Displacement parametersBiso mean: 31.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 58 326 2800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3279 303 9.649 %
Rwork0.3054 2818 -
obs--100 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8

+
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