[English] 日本語
Yorodumi
- PDB-3rhb: Crystal structure of the apo form of glutaredoxin C5 from Arabido... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rhb
TitleCrystal structure of the apo form of glutaredoxin C5 from Arabidopsis thaliana
ComponentsGlutaredoxin-C5, chloroplastic
KeywordsOXIDOREDUCTASE / Thioredoxin fold / thiol-disulfide oxidoreductase / glutaredoxin
Function / homology
Function and homology information


iron-sulfur cluster assembly / chloroplast
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutaredoxin-C5, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRoret, T. / Couturier, J. / Tsan, P. / Jacquot, J.P. / Rouhier, N. / Didierjean, C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Arabidopsis chloroplastic glutaredoxin c5 as a model to explore molecular determinants for iron-sulfur cluster binding into glutaredoxins.
Authors: Couturier, J. / Stroher, E. / Albetel, A.N. / Roret, T. / Muthuramalingam, M. / Tarrago, L. / Seidel, T. / Tsan, P. / Jacquot, J.P. / Johnson, M.K. / Dietz, K.J. / Didierjean, C. / Rouhier, N.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Glutaredoxin-C5, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0945
Polymers12,4981
Non-polymers5964
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.527, 39.020, 37.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-149-

HOH

21A-192-

HOH

DetailsAUTHORS STATE THAT THE PROTEIN IS MONOMERIC IN SOLUTION ACCORDING TO ANALYTICAL GEL FILTRATION ANALYSES.

-
Components

#1: Protein Glutaredoxin-C5, chloroplastic / AtGrxC5


Mass: 12498.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GRXC5, At4g28730, F16A16.160 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GWS0
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34.03 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 1.6 M ammonium sulfate, 500 mM lithium chloride, Microbatch, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2010 / Details: mirrors
RadiationMonochromator: 111 SILICON SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.2→33.25 Å / Num. obs: 26715 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.9

-
Processing

Software
NameVersionClassification
Xnemodata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZ9

3fz9


Resolution: 1.2→33.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.015 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17585 1423 5.1 %RANDOM
Rwork0.15029 ---
all0.15029 26715 --
obs0.15029 26715 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 35 108 927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022884
X-RAY DIFFRACTIONr_angle_refined_deg2.2092.0171206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20224.68832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1815166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.133155
X-RAY DIFFRACTIONr_chiral_restr0.1340.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021641
X-RAY DIFFRACTIONr_mcbond_it2.9321.5537
X-RAY DIFFRACTIONr_mcangle_it4.2692889
X-RAY DIFFRACTIONr_scbond_it5.793347
X-RAY DIFFRACTIONr_scangle_it8.2664.5317
X-RAY DIFFRACTIONr_rigid_bond_restr2.7753814
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 78 -
Rwork0.186 1288 -
obs--62.18 %

+
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