[English] 日本語
Yorodumi
- PDB-7pwe: Crystal structure of the glutaredoxin/ferredoxin disulfide reduct... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pwe
TitleCrystal structure of the glutaredoxin/ferredoxin disulfide reductase fusion protein from Desulfotalea psychrophila Lsv54
ComponentsFerredoxin-thioredoxin reductase subunit B
KeywordsUNKNOWN FUNCTION / glutaredoxin ferredoxin disulfide reductase ferredocxin thioredoxin reductase enzyme
Function / homology
Function and homology information


: / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily
Similarity search - Domain/homology
IMIDAZOLE / IRON/SULFUR CLUSTER / Ferredoxin:thioredoxin reductase
Similarity search - Component
Biological speciesDesulfotalea psychrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.077 Å
AuthorsDidierjean, C. / Mathiot, S. / Rouhier, N.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Inorganics / Year: 2022
Title: Crystal structure of the glutaredoxin/ferredoxin disulfide reductase fusion protein from Desulfotalea psychrophila Lsv54
Authors: Zannini, F. / Mathiot, S. / Couturier, J. / Didierjean, C. / Rouhier, N.
History
DepositionOct 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferredoxin-thioredoxin reductase subunit B
B: Ferredoxin-thioredoxin reductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,79610
Polymers45,6782
Non-polymers1,1188
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-29 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.6, 49.3, 86
Angle α, β, γ (deg.)90, 116.5, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

-
Components

#1: Protein Ferredoxin-thioredoxin reductase subunit B


Mass: 22838.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfotalea psychrophila (strain LSv54 / DSM 12343) (bacteria)
Strain: LSv54 / DSM 12343 / Gene: DP2155 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6AL91, ferredoxin:thioredoxin reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8
Details: 30% MPD, 10% PEG4000, and 0.1M Imidazole-HCl (JBScreen Classic condition JBS6 B2)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.08→41.42 Å / Num. obs: 54939 / % possible obs: 98.7 % / Redundancy: 3 % / Rrim(I) all: 0.037 / Net I/σ(I): 22.81
Reflection shellResolution: 2.08→2.13 Å / Mean I/σ(I) obs: 5.84 / Num. unique obs: 4067 / Rrim(I) all: 0.236

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.077→41.42 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1353 -RANDOM
Rwork0.1911 ---
obs0.1926 28102 99.4 %-
Displacement parametersBiso mean: 37.85 Å2
Baniso -1Baniso -2Baniso -3
1-4.4138 Å20 Å213.0982 Å2
2--1.6577 Å20 Å2
3----6.0715 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.077→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 46 327 3506
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083353HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914538HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1228SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it3353HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3181SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion16.01
LS refinement shellResolution: 2.08→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3605 33 -
Rwork0.2195 --
obs0.2279 563 94.53 %

+
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://pdbjlvh1.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