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- PDB-3d6i: Structure of the Thioredoxin-like Domain of Yeast Glutaredoxin 3 -

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Basic information

Entry
Database: PDB / ID: 3d6i
TitleStructure of the Thioredoxin-like Domain of Yeast Glutaredoxin 3
ComponentsMonothiol glutaredoxin-3
KeywordsOXIDOREDUCTASE / thioredoxin-like / glutaredoxin / Electron transport / Redox-active center / Transport
Function / homology
Function and homology information


negative regulation of transcription regulatory region DNA binding / disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / actin cytoskeleton organization / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / nucleus ...negative regulation of transcription regulatory region DNA binding / disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / iron-sulfur cluster binding / 2 iron, 2 sulfur cluster binding / actin cytoskeleton organization / intracellular iron ion homeostasis / RNA polymerase II-specific DNA-binding transcription factor binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Monothiol glutaredoxin-3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsLebioda, L. / Gibson, L.M. / Dingra, N.N. / Outten, C.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of the thioredoxin-like domain of yeast glutaredoxin 3.
Authors: Gibson, L.M. / Dingra, N.N. / Outten, C.E. / Lebioda, L.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monothiol glutaredoxin-3
B: Monothiol glutaredoxin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3384
Polymers25,1462
Non-polymers1922
Water2,612145
1
A: Monothiol glutaredoxin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6692
Polymers12,5731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monothiol glutaredoxin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6692
Polymers12,5731
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.906, 48.611, 55.294
Angle α, β, γ (deg.)90.000, 116.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Monothiol glutaredoxin-3


Mass: 12573.053 Da / Num. of mol.: 2 / Fragment: Thioredoxin-like Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GRX3, YDR098C, YD8557.05C / Production host: Escherichia coli (E. coli) / References: UniProt: Q03835
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M MOPS, 20mM 2-ME, 68% ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 35163 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Χ2: 2.83 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.347 / Num. unique all: 2534 / Χ2: 1.829 / % possible all: 69.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SERGUIcontrol programdata collection
HKL-2000data reduction
AMoREphasing
RefinementStarting model: PDB Entry 1ERT

1ert


Resolution: 1.5→49.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.538 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1752 5 %RANDOM
Rwork0.223 ---
obs0.225 35147 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.1 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 10 145 1876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221763
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9662393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0775215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3526.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30315296
X-RAY DIFFRACTIONr_chiral_restr0.0780.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021288
X-RAY DIFFRACTIONr_nbd_refined0.2080.2767
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.210
X-RAY DIFFRACTIONr_mcbond_it1.1071.51118
X-RAY DIFFRACTIONr_mcangle_it1.84721770
X-RAY DIFFRACTIONr_scbond_it2.7353726
X-RAY DIFFRACTIONr_scangle_it4.0024.5622
LS refinement shellResolution: 1.5→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 98 -
Rwork0.307 1646 -
all-1744 -
obs-1646 65.74 %

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