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- PDB-7ncw: Crystal structure of oxidized glutaredoxin 2 from Chlamydomonas r... -

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Basic information

Entry
Database: PDB / ID: 7ncw
TitleCrystal structure of oxidized glutaredoxin 2 from Chlamydomonas reinhardtii
ComponentsGlutaredoxin, CPYC type
KeywordsOXIDOREDUCTASE / Chlamydomonas reinhardtii glutaredoxin
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / cellular response to oxidative stress / cytoplasm
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: Antioxidants (Basel) / Year: 2021
Title: Atypical Iron-Sulfur Cluster Binding, Redox Activity and Structural Properties of Chlamydomonas reinhardtii Glutaredoxin 2.
Authors: Roret, T. / Zhang, B. / Moseler, A. / Dhalleine, T. / Gao, X.H. / Couturier, J. / Lemaire, S.D. / Didierjean, C. / Johnson, M.K. / Rouhier, N.
History
DepositionJan 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin, CPYC type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4162
Polymers11,3571
Non-polymers591
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.383, 45.383, 104.238
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

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Components

#1: Protein Glutaredoxin, CPYC type


Mass: 11356.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cys56 residue is oxidized into a sulfenic acid. / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: GRX2, CHLRE_12g550400v5, CHLREDRAFT_195611 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8IYH1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 30% (w/v) PEG 8000 0.1 M sodium cacodylate pH 6.5 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.540562 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 2.4→14.7 Å / Num. obs: 5212 / % possible obs: 99.1 % / Redundancy: 6 % / Biso Wilson estimate: 21.36 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3 / Num. unique obs: 723 / Rpim(I) all: 0.206 / Rrim(I) all: 0.435

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Processing

Software
NameVersionClassification
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
Cootmodel building
MOLREPphasing
PHENIX1.18.2-3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FLS

2fls


Resolution: 2.4→14.3 Å / SU ML: 0.1968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2294 236 4.55 %
Rwork0.1972 4946 -
obs0.1986 5182 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 4 92 890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017805
X-RAY DIFFRACTIONf_angle_d0.42091084
X-RAY DIFFRACTIONf_chiral_restr0.0399125
X-RAY DIFFRACTIONf_plane_restr0.0016143
X-RAY DIFFRACTIONf_dihedral_angle_d16.0456295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-3.020.23841060.2172416X-RAY DIFFRACTION99.06
3.02-14.30.22571300.18752530X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: 3.57454576379 Å / Origin y: -19.7896406801 Å / Origin z: -9.96521343859 Å
111213212223313233
T0.111315237249 Å2-0.0335570519926 Å20.015081216084 Å2-0.16022619065 Å2-0.0517122499514 Å2--0.116662697837 Å2
L2.64686662425 °21.02895446435 °2-0.138438915336 °2-2.21116191873 °20.280631033045 °2--3.43751970491 °2
S-0.0313239658825 Å °-0.00976278786418 Å °0.0266792798022 Å °-0.0844679162372 Å °-0.0864824301464 Å °0.124874321699 Å °0.0338668374454 Å °-0.451915807236 Å °-0.0223710170805 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 107)

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