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- PDB-3gx0: Crystal Structure of GSH-dependent Disulfide bond Oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 3gx0
TitleCrystal Structure of GSH-dependent Disulfide bond Oxidoreductase
ComponentsGST-like protein yfcG
KeywordsTRANSFERASE / Glutathione / Glutathione disulfide / disulfide bond oxidoreductase
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / disulfide oxidoreductase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / response to oxidative stress / protein homodimerization activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
OXIDIZED GLUTATHIONE DISULFIDE / Disulfide-bond oxidoreductase YfcG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLadner, J.E. / Harp, J.M. / Wadington, M.C. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2009
Title: Analysis of the structure and function of YfcG from Escherichia coli reveals an efficient and unique disulfide bond reductase.
Authors: Wadington, M.C. / Ladner, J.E. / Stourman, N.V. / Harp, J.M. / Armstrong, R.N.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GST-like protein yfcG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1582
Polymers24,5461
Non-polymers6131
Water1,67593
1
A: GST-like protein yfcG
hetero molecules

A: GST-like protein yfcG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3174
Polymers49,0922
Non-polymers1,2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6110 Å2
ΔGint-24 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 68.490, 111.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GST-like protein yfcG / GSH-dependent disulfide bond oxidoreductase


Mass: 24545.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: yfcG / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77526
#2: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE


Mass: 612.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growMethod: vapor diffusion, hanging drop
Details: Protein in 20 mM potassium dihydrogen phosphate, 2 mM DTT, 1mM EDTA, 10 mM glutathione. Well solution: 20% w/v PEG 3000, 100 mM acetate., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 1, 2007 / Details: Montel graded multilayer optics from Bruker Nonius
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12571 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.35 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å9.99 Å
Translation3 Å9.99 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.966 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24981 584 4.9 %RANDOM
Rwork0.19068 ---
obs0.1935 11342 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---1.01 Å20 Å2
3---2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 40 93 1791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221749
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9582380
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6915205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99823.21484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64715274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9451513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2852
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21175
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9051.51043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59421643
X-RAY DIFFRACTIONr_scbond_it2.243815
X-RAY DIFFRACTIONr_scangle_it3.4274.5736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.423 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.357 93 -
Rwork0.249 1486 -
obs--90.96 %

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