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- PDB-4zbd: Crystal structure of the glutathione transferase URE2P6 from Phan... -

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Basic information

Entry
Database: PDB / ID: 4zbd
TitleCrystal structure of the glutathione transferase URE2P6 from Phanerochaete chrysosporium in complex with glutathione reduced by X-ray irradiation at 100K
ComponentsPcUre2p6
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / GST FOLD / OXYDIZED GLUTATHIONE
Function / homology
Function and homology information


glutathione transferase
Similarity search - Function
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 / 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 / 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 / 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
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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

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Assembly

Deposited unit
A: PcUre2p6
B: PcUre2p6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3656
Polymers51,1362
Non-polymers1,2294
Water12,574698
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-34 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.455, 50.096, 97.141
Angle α, β, γ (deg.)90.00, 96.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

21B-747-

HOH

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Components

#1: Protein PcUre2p6


Mass: 25567.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R4I981*PLUS
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 278 K / Method: microbatch / Details: 30 % PEG4000, 10mM TRIS pH8.5, 0.2M Sodium 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: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.1→48.3 Å / Num. obs: 198807 / % possible obs: 95.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.073 / Net I/σ(I): 16.4
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.16 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZB8

4zb8


Resolution: 1.12→26.646 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1441 8324 5.03 %
Rwork0.1171 --
obs0.1184 165517 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.12→26.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 80 698 4360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013835
X-RAY DIFFRACTIONf_angle_d1.55202
X-RAY DIFFRACTIONf_dihedral_angle_d14.0591395
X-RAY DIFFRACTIONf_chiral_restr0.091530
X-RAY DIFFRACTIONf_plane_restr0.01672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.13270.11933060.10345043X-RAY DIFFRACTION94
1.1327-1.14610.13122810.0994980X-RAY DIFFRACTION94
1.1461-1.160.13012940.09995099X-RAY DIFFRACTION94
1.16-1.17470.14182520.10175128X-RAY DIFFRACTION94
1.1747-1.19020.11632730.10215018X-RAY DIFFRACTION94
1.1902-1.20650.11782390.10045167X-RAY DIFFRACTION94
1.2065-1.22370.14012700.10295101X-RAY DIFFRACTION95
1.2237-1.2420.13352900.10365089X-RAY DIFFRACTION95
1.242-1.26140.13722820.10335203X-RAY DIFFRACTION95
1.2614-1.28210.1352570.10115113X-RAY DIFFRACTION95
1.2821-1.30420.13592690.10095200X-RAY DIFFRACTION96
1.3042-1.32790.13222800.10145174X-RAY DIFFRACTION96
1.3279-1.35340.14592840.10165193X-RAY DIFFRACTION96
1.3534-1.38110.13222860.10535175X-RAY DIFFRACTION96
1.3811-1.41110.13772730.10275246X-RAY DIFFRACTION97
1.4111-1.44390.14222750.10275230X-RAY DIFFRACTION97
1.4439-1.480.1232600.10035298X-RAY DIFFRACTION97
1.48-1.520.13132870.09915295X-RAY DIFFRACTION97
1.52-1.56470.14883080.10165261X-RAY DIFFRACTION98
1.5647-1.61520.12752920.09935282X-RAY DIFFRACTION98
1.6152-1.6730.12772600.10465311X-RAY DIFFRACTION98
1.673-1.73990.12842690.1045318X-RAY DIFFRACTION98
1.7399-1.81910.12522900.11095313X-RAY DIFFRACTION98
1.8191-1.9150.14262800.1135366X-RAY DIFFRACTION99
1.915-2.03490.12552590.11675387X-RAY DIFFRACTION99
2.0349-2.1920.14952780.11895388X-RAY DIFFRACTION99
2.192-2.41240.13733240.11985371X-RAY DIFFRACTION99
2.4124-2.76120.15282420.13295457X-RAY DIFFRACTION99
2.7612-3.47760.18092760.14265448X-RAY DIFFRACTION99
3.4776-26.65310.1742880.14835539X-RAY DIFFRACTION98

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