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- PDB-4zb6: Crystal structure of glutathione transferase URE2P4 from Phaneroc... -

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Basic information

Entry
Database: PDB / ID: 4zb6
TitleCrystal structure of glutathione transferase URE2P4 from Phanerochaete chrysosporium in complex with oxidized glutathione.
ComponentsPcUre2p4
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / GST FOLD / OXYDIZED GLUTATHIONE
Function / homology
Function and homology information


Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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 / PcUre2p4
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: Fungal Genet. Biol. / Year: 2015
Title: Evolutionary divergence of Ure2pA glutathione transferases in wood degrading fungi.
Authors: Roret, T. / Thuillier, A. / Favier, F. / Gelhaye, E. / Didierjean, C. / Morel-Rouhier, M.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: PcUre2p4
B: PcUre2p4
C: PcUre2p4
D: PcUre2p4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,13412
Polymers102,5924
Non-polymers2,5428
Water20,2311123
1
A: PcUre2p4
B: PcUre2p4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5676
Polymers51,2962
Non-polymers1,2714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-36 kcal/mol
Surface area17990 Å2
MethodPISA
2
C: PcUre2p4
D: PcUre2p4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5676
Polymers51,2962
Non-polymers1,2714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-37 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.437, 94.059, 104.627
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
PcUre2p4


Mass: 25647.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4I980*PLUS
#2: Chemical
ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE / Glutathione disulfide


Mass: 612.631 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#3: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1123 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 278 K / Method: microbatch
Details: 30 % PEG4000, 0.1M Sodium Acetate pH4.6, 0.2M Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. obs: 84906 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 3.3 / Num. unique all: 12133 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZB8

4zb8


Resolution: 1.801→47 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 4235 4.99 %
Rwork0.1634 --
obs0.1647 84797 99.81 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.862 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3233 Å2-0 Å20 Å2
2---5.7094 Å2-0 Å2
3---0.5378 Å2
Refinement stepCycle: LAST / Resolution: 1.801→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7146 0 164 1123 8433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047524
X-RAY DIFFRACTIONf_angle_d0.89310221
X-RAY DIFFRACTIONf_dihedral_angle_d15.3772723
X-RAY DIFFRACTIONf_chiral_restr0.0651059
X-RAY DIFFRACTIONf_plane_restr0.0041315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.82110.26721330.26362528X-RAY DIFFRACTION96
1.8211-1.84250.27181320.23512678X-RAY DIFFRACTION100
1.8425-1.8650.26711520.23182637X-RAY DIFFRACTION100
1.865-1.88860.27331290.2352703X-RAY DIFFRACTION100
1.8886-1.91350.27941240.18792655X-RAY DIFFRACTION100
1.9135-1.93970.22411390.19072679X-RAY DIFFRACTION100
1.9397-1.96740.2491350.19132653X-RAY DIFFRACTION100
1.9674-1.99680.21151360.18042654X-RAY DIFFRACTION100
1.9968-2.0280.21111400.16862645X-RAY DIFFRACTION100
2.028-2.06120.18391490.17282663X-RAY DIFFRACTION100
2.0612-2.09670.19951300.16912677X-RAY DIFFRACTION100
2.0967-2.13490.19061310.16962689X-RAY DIFFRACTION100
2.1349-2.17590.21291210.16082659X-RAY DIFFRACTION100
2.1759-2.22030.17671520.15872656X-RAY DIFFRACTION100
2.2203-2.26860.20811370.15982705X-RAY DIFFRACTION100
2.2686-2.32140.16651330.15262662X-RAY DIFFRACTION100
2.3214-2.37950.17691590.14432666X-RAY DIFFRACTION100
2.3795-2.44380.18281280.15142713X-RAY DIFFRACTION100
2.4438-2.51570.18861320.15652667X-RAY DIFFRACTION100
2.5157-2.59690.20271780.16212657X-RAY DIFFRACTION100
2.5969-2.68970.19481440.1592696X-RAY DIFFRACTION100
2.6897-2.79740.1871660.15772658X-RAY DIFFRACTION100
2.7974-2.92470.19911590.16372668X-RAY DIFFRACTION100
2.9247-3.07880.18931460.1632708X-RAY DIFFRACTION100
3.0788-3.27170.18651660.15572700X-RAY DIFFRACTION100
3.2717-3.52420.1811240.14922716X-RAY DIFFRACTION100
3.5242-3.87870.16151170.14042768X-RAY DIFFRACTION100
3.8787-4.43960.1441560.1342731X-RAY DIFFRACTION100
4.4396-5.5920.1651460.14822774X-RAY DIFFRACTION100
5.592-47.04550.17141410.18362897X-RAY DIFFRACTION99

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