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- PDB-5y4u: Crystal structure of Grx domain of Grx3 from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5y4u
TitleCrystal structure of Grx domain of Grx3 from Saccharomyces cerevisiae
ComponentsMonothiol glutaredoxin-3
KeywordsOXIDOREDUCTASE / monothiol glutaredoxin / glutathione
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 / metal ion binding ...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 / metal ion binding / nucleus / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChi, C.B. / Tang, Y.J. / Zhang, J.H. / Dai, Y.N. / Abdalla, M. / Chen, Y.X. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2012CB911002 China
National Natural Science Foundation31400629 China
CitationJournal: J.Mol.Biol. / Year: 2018
Title: Structural and Biochemical Insights into the Multiple Functions of Yeast Grx3.
Authors: Chi, C.B. / Tang, Y. / Zhang, J. / Dai, Y.N. / Abdalla, M. / Chen, Y. / Zhou, C.Z.
History
DepositionAug 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monothiol glutaredoxin-3


Theoretical massNumber of molelcules
Total (without water)13,4411
Polymers13,4411
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5870 Å2
Unit cell
Length a, b, c (Å)41.195, 45.749, 45.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Monothiol glutaredoxin-3


Mass: 13441.141 Da / Num. of mol.: 1 / Fragment: UNP residues 144-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GRX3, YDR098C, YD8557.05C / Production host: Escherichia coli (E. coli) / References: UniProt: Q03835
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.61 Å3/Da / Density % sol: 23.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl, pH 8.0, 2 M Ammonium sulfate / PH range: 7.8 - 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 10493 / % possible obs: 97 % / Redundancy: 4.2 % / Net I/σ(I): 20.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZYW
Resolution: 1.7→25.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.689 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22948 476 4.9 %RANDOM
Rwork0.17999 ---
obs0.18234 9234 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.346 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.7→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms803 0 0 62 865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019822
X-RAY DIFFRACTIONr_bond_other_d0.0010.02792
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9681106
X-RAY DIFFRACTIONr_angle_other_deg0.88131825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.839598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11124.04842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29215148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.796156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021927
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2472.067395
X-RAY DIFFRACTIONr_mcbond_other2.0942.052394
X-RAY DIFFRACTIONr_mcangle_it3.2113.082492
X-RAY DIFFRACTIONr_mcangle_other3.2263.096493
X-RAY DIFFRACTIONr_scbond_it3.2992.427427
X-RAY DIFFRACTIONr_scbond_other3.2982.427427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.873.521615
X-RAY DIFFRACTIONr_long_range_B_refined6.01817.287943
X-RAY DIFFRACTIONr_long_range_B_other6.00316.884919
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 35 -
Rwork0.229 639 -
obs--93.74 %

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