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- PDB-4f0c: Crystal structure of the glutathione transferase URE2P5 from Phan... -

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Basic information

Entry
Database: PDB / ID: 4f0c
TitleCrystal structure of the glutathione transferase URE2P5 from Phanerochaete chrysosporium
ComponentsGlutathione transferase
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / GST fold / oxydized glutathione
Function / homology
Function and homology information


transferase activity
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
OXIDIZED GLUTATHIONE DISULFIDE / Glutathione transferase Ure2p5
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsDidierjean, C. / Favier, F. / Roret, T.
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
DepositionMay 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,80510
Polymers26,4361
Non-polymers1,3699
Water4,306239
1
A: Glutathione transferase
hetero molecules

A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,61120
Polymers52,8722
Non-polymers2,73818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3620 Å2
ΔGint-24 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.101, 73.101, 97.105
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glutathione transferase


Mass: 26436.141 Da / Num. of mol.: 1 / Fragment: PcUre2p5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: I7B368*PLUS
#2: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE


Mass: 612.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 277 K / pH: 7.7
Details: 3.5M Ammonium Sulfate, pH 7.7, MICROBATCH, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97993 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2011 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97993 Å / Relative weight: 1
ReflectionResolution: 1.9→48.55 Å / Num. all: 23921 / Num. obs: 23921 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F0B

4f0b


Resolution: 1.901→31.654 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.169 1215 5.09 %RANDOM
Rwork0.1407 ---
all0.1422 23877 --
obs0.1422 23877 98.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.687 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0769 Å2-0 Å2-0 Å2
2--0.0769 Å20 Å2
3----0.1538 Å2
Refinement stepCycle: LAST / Resolution: 1.901→31.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 83 239 2188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132035
X-RAY DIFFRACTIONf_angle_d1.2962764
X-RAY DIFFRACTIONf_dihedral_angle_d17.334731
X-RAY DIFFRACTIONf_chiral_restr0.095285
X-RAY DIFFRACTIONf_plane_restr0.008352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.97740.22531480.18132458X-RAY DIFFRACTION99
1.9774-2.06740.17181420.15052503X-RAY DIFFRACTION100
2.0674-2.17630.18611190.1272523X-RAY DIFFRACTION100
2.1763-2.31260.14951240.12732526X-RAY DIFFRACTION100
2.3126-2.49110.17841310.13482537X-RAY DIFFRACTION100
2.4911-2.74170.18651350.14232524X-RAY DIFFRACTION100
2.7417-3.13810.16551610.14822518X-RAY DIFFRACTION100
3.1381-3.95250.15841440.132523X-RAY DIFFRACTION98
3.9525-31.6580.15341110.14532550X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0881-0.4390.081.92270.25981.3547-0.0546-0.11350.00030.2895-0.03010.39740.0195-0.24320.06020.11290.02260.0540.0956-0.01270.11292.078328.599112.9992
22.3986-0.0917-0.16371.92630.12730.3034-0.0446-0.11860.18040.16850.0901-0.0969-0.10190.05080.0060.12540.0293-0.0110.0939-0.00740.076418.375532.33839.8286
31.134-0.32360.3211.8692-0.16340.9105-0.0608-0.1578-0.38870.24390.08070.0660.0911-0.05620.00750.11160.0410.01250.06050.04220.105816.040610.50519.4782
45.17081.69510.25733.46080.34291.0142-0.0084-0.5752-0.03080.5891-0.1080.4390.2494-0.175-0.10790.41320.00980.07430.20130.04950.01344.866218.463425.5899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:73)
2X-RAY DIFFRACTION2chain 'A' and (resseq 74:95)
3X-RAY DIFFRACTION3chain 'A' and (resseq 96:210)
4X-RAY DIFFRACTION4chain 'A' and (resseq 211:229)

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