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- PDB-5j3r: Crystal structure of yeast monothiol glutaredoxin Grx6 in complex... -

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Basic information

Entry
Database: PDB / ID: 5j3r
TitleCrystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe-2S] cluster
ComponentsMonothiol glutaredoxin-6
KeywordsOXIDOREDUCTASE / glutaredoxin / iron-sulfur cluster / Saccharomyces cerevisiae
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / glutathione-disulfide reductase (NADPH) activity / fungal-type vacuole / cis-Golgi network / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / Golgi lumen / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / intracellular iron ion homeostasis ...glutathione disulfide oxidoreductase activity / glutathione-disulfide reductase (NADPH) activity / fungal-type vacuole / cis-Golgi network / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / Golgi lumen / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / intracellular iron ion homeostasis / iron ion binding / endoplasmic reticulum membrane / Golgi apparatus / membrane / cytoplasm
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
FE2/S2 (INORGANIC) CLUSTER / GLUTATHIONE / Monothiol glutaredoxin-6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsAbdalla, M. / Dai, Y.-N. / Chi, C.-B. / Cheng, W. / Cao, D.-D. / Zhou, K. / Ali, W. / Chen, Y. / Zhou, C.-Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2012CB911002 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of yeast monothiol glutaredoxin Grx6 in complex with a glutathione-coordinated [2Fe-2S] cluster
Authors: Abdalla, M. / Dai, Y.-N. / Chi, C.-B. / Cheng, W. / Cao, D.-D. / Zhou, K. / Ali, W. / Chen, Y. / Zhou, C.-Z.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monothiol glutaredoxin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3083
Polymers22,8251
Non-polymers4832
Water95553
1
A: Monothiol glutaredoxin-6
hetero molecules

A: Monothiol glutaredoxin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6156
Polymers45,6492
Non-polymers9664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2380 Å2
ΔGint-56 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.657, 58.657, 161.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-301-

FES

21A-301-

FES

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Components

#1: Protein Monothiol glutaredoxin-6


Mass: 22824.502 Da / Num. of mol.: 1 / Fragment: UNP residues 37-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: GRX6 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12438
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium, 0.8 M potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 10929 / % possible obs: 99.4 % / Redundancy: 12.6 % / Net I/σ(I): 23.5
Reflection shellResolution: 2.45→2.54 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4N

3l4n


Resolution: 2.46→28.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.466 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23005 525 4.8 %RANDOM
Rwork0.1964 ---
obs0.19799 10375 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.46→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 24 53 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02958
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9961286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.42925.45544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.248153
X-RAY DIFFRACTIONr_chiral_restr0.0880.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021707
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.456→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 34 -
Rwork0.274 622 -
obs--96.19 %

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