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- PDB-5f05: Crystal structure of glutathione transferase F5 from Populus tric... -

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Basic information

Entry
Database: PDB / ID: 5f05
TitleCrystal structure of glutathione transferase F5 from Populus trichocarpa
ComponentsPhi class glutathione transferase GSTF5
KeywordsTRANSFERASE / glutathione / ligandin
Function / homology
Function and homology information


toxin catabolic process / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione transferase family / 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-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione transferase family / 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 / TRIETHYLENE GLYCOL / glutathione transferase
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDidierjean, C. / Rouhier, N. / Pegeot, H. / Gense, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-LABX-0002-01 France
CitationJournal: FEBS J. / Year: 2017
Title: Structural plasticity among glutathione transferase Phi members: natural combination of catalytic residues confers dual biochemical activities.
Authors: Pegeot, H. / Mathiot, S. / Perrot, T. / Gense, F. / Hecker, A. / Didierjean, C. / Rouhier, N.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: 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_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Phi class glutathione transferase GSTF5
B: Phi class glutathione transferase GSTF5
C: Phi class glutathione transferase GSTF5
D: Phi class glutathione transferase GSTF5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,44918
Polymers92,3654
Non-polymers3,08414
Water15,763875
1
A: Phi class glutathione transferase GSTF5
B: Phi class glutathione transferase GSTF5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,77110
Polymers46,1822
Non-polymers1,5888
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-31 kcal/mol
Surface area16640 Å2
MethodPISA
2
C: Phi class glutathione transferase GSTF5
D: Phi class glutathione transferase GSTF5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6788
Polymers46,1822
Non-polymers1,4966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-23 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.459, 85.952, 88.520
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Phi class glutathione transferase GSTF5


Mass: 23091.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0483s00220g / Production host: Escherichia coli (E. coli) / References: UniProt: D2WL63

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Non-polymers , 7 types, 889 molecules

#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 44.63 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8.5 / Details: 30% PEG 4000, Tris HCl, 0.2 M Mg chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979961 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979961 Å / Relative weight: 1
ReflectionResolution: 1.7→49.06 Å / Num. obs: 88400 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 3 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RI6

4ri6


Resolution: 1.7→43.35 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 4427 5.01 %Random selection
Rwork0.144 ---
obs0.1459 88304 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6500 0 203 875 7578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156972
X-RAY DIFFRACTIONf_angle_d1.5429472
X-RAY DIFFRACTIONf_dihedral_angle_d16.3112556
X-RAY DIFFRACTIONf_chiral_restr0.0651064
X-RAY DIFFRACTIONf_plane_restr0.0091210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71940.25621210.20812475X-RAY DIFFRACTION89
1.7194-1.73960.2661350.20262811X-RAY DIFFRACTION100
1.7396-1.76080.2511600.19032793X-RAY DIFFRACTION100
1.7608-1.78310.23541460.17312759X-RAY DIFFRACTION100
1.7831-1.80660.20431370.16282828X-RAY DIFFRACTION100
1.8066-1.83130.20991490.16362779X-RAY DIFFRACTION100
1.8313-1.85750.22221390.17122793X-RAY DIFFRACTION100
1.8575-1.88520.21711490.1662816X-RAY DIFFRACTION100
1.8852-1.91460.23891320.16322806X-RAY DIFFRACTION100
1.9146-1.9460.2181320.16222836X-RAY DIFFRACTION100
1.946-1.97960.18961580.15242752X-RAY DIFFRACTION100
1.9796-2.01560.19461550.14722810X-RAY DIFFRACTION100
2.0156-2.05440.20951480.14192799X-RAY DIFFRACTION100
2.0544-2.09630.17751610.14692818X-RAY DIFFRACTION100
2.0963-2.14190.16921620.13762736X-RAY DIFFRACTION100
2.1419-2.19170.18311530.14042824X-RAY DIFFRACTION100
2.1917-2.24650.20331570.13932779X-RAY DIFFRACTION100
2.2465-2.30720.17781240.13422831X-RAY DIFFRACTION100
2.3072-2.37510.16581600.12092833X-RAY DIFFRACTION100
2.3751-2.45180.16441490.12512785X-RAY DIFFRACTION100
2.4518-2.53940.17451530.12792803X-RAY DIFFRACTION100
2.5394-2.64110.18281360.13432803X-RAY DIFFRACTION100
2.6411-2.76120.17231510.13262834X-RAY DIFFRACTION100
2.7612-2.90680.18511400.13722820X-RAY DIFFRACTION100
2.9068-3.08890.16471540.13112803X-RAY DIFFRACTION100
3.0889-3.32730.1621380.13872835X-RAY DIFFRACTION100
3.3273-3.6620.1621590.13432824X-RAY DIFFRACTION100
3.662-4.19150.14511650.11872824X-RAY DIFFRACTION100
4.1915-5.27930.1451430.13512830X-RAY DIFFRACTION100
5.2793-43.36440.1761610.18412838X-RAY DIFFRACTION98

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