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- PDB-7ncv: Crystal structure of reduced glutaredoxin 2 from Chlamydomonas re... -

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Basic information

Entry
Database: PDB / ID: 7ncv
TitleCrystal structure of reduced 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)11,4624
Polymers11,3571
Non-polymers1053
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-18 kcal/mol
Surface area5590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.648, 45.648, 104.667
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-348-

HOH

21A-433-

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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9785 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→39.53 Å / Num. obs: 20838 / % possible obs: 96.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.42 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.023 / Rrim(I) all: 0.049 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2951 / Rpim(I) all: 0.202 / Rrim(I) all: 0.414

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Processing

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

2fls


Resolution: 1.5→39.53 Å / SU ML: 0.103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1799 1070 5.13 %
Rwork0.1528 19768 -
obs0.1541 20838 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.95 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 6 153 953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145827
X-RAY DIFFRACTIONf_angle_d1.3691115
X-RAY DIFFRACTIONf_chiral_restr0.0875127
X-RAY DIFFRACTIONf_plane_restr0.0088148
X-RAY DIFFRACTIONf_dihedral_angle_d22.1243308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.570.22771510.1982399X-RAY DIFFRACTION98
1.57-1.650.21091320.16882431X-RAY DIFFRACTION99.88
1.65-1.760.18621280.15552463X-RAY DIFFRACTION99.92
1.76-1.890.17051310.13542419X-RAY DIFFRACTION99.92
1.89-2.080.15681340.13752487X-RAY DIFFRACTION100
2.08-2.380.17071330.14152465X-RAY DIFFRACTION99.96
2.38-30.1711360.16062505X-RAY DIFFRACTION100
3-39.530.18851250.15392599X-RAY DIFFRACTION97.49
Refinement TLS params.Method: refined / Origin x: -15.462756453 Å / Origin y: -13.1805433618 Å / Origin z: 7.42526830367 Å
111213212223313233
T0.155406946185 Å20.0395852199503 Å2-0.0212360544844 Å2-0.158849513283 Å2-0.030017663018 Å2--0.152522957891 Å2
L1.91864812807 °20.0449476415776 °20.041828970854 °2-0.997980989872 °2-0.0374951082261 °2--2.2102910603 °2
S-0.108366604519 Å °-0.0582758337838 Å °0.12912424951 Å °-0.0274258134659 Å °-0.0249694891994 Å °0.0152037393072 Å °-0.294652926488 Å °-0.147577291491 Å °-0.0069942408931 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 107)

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