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- PDB-5f06: Crystal structure of glutathione transferase F7 from Populus tric... -

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Basic information

Entry
Database: PDB / ID: 5f06
TitleCrystal structure of glutathione transferase F7 from Populus trichocarpa
ComponentsGlutathione S-transferase family protein
KeywordsTRANSFERASE / glutathione / ligandin
Function / homology
Function and homology information


toxin catabolic process / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / 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 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-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 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 speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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: Glutathione S-transferase family protein
B: Glutathione S-transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7075
Polymers48,9962
Non-polymers7113
Water13,619756
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-49 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.104, 90.365, 97.149
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 Glutathione S-transferase family protein


Mass: 24498.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_0002s20900g / Production host: Escherichia coli (E. coli) / References: UniProt: U5GTL0
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7.5
Details: 16% PEG 4000, 10% 2-propanol, Na Hepes pH 7.5, 0.2 AS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979769 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979769 Å / Relative weight: 1
ReflectionResolution: 1.73→48.57 Å / Num. obs: 50544 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.1
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.664 / % possible all: 100

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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: 1.8→46.42 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2245 5.04 %Random selection
Rwork0.179 ---
obs0.1807 44559 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 45 756 4207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063634
X-RAY DIFFRACTIONf_angle_d0.8614952
X-RAY DIFFRACTIONf_dihedral_angle_d12.6171365
X-RAY DIFFRACTIONf_chiral_restr0.033538
X-RAY DIFFRACTIONf_plane_restr0.004641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83910.2331540.2042599X-RAY DIFFRACTION100
1.8391-1.88190.26271460.21122627X-RAY DIFFRACTION100
1.8819-1.9290.40131310.36222506X-RAY DIFFRACTION96
1.929-1.98110.2431330.21732599X-RAY DIFFRACTION99
1.9811-2.03940.22531330.1792630X-RAY DIFFRACTION100
2.0394-2.10530.23181530.17822642X-RAY DIFFRACTION100
2.1053-2.18050.2021470.17772612X-RAY DIFFRACTION100
2.1805-2.26780.32431240.27732540X-RAY DIFFRACTION95
2.2678-2.3710.24631270.18172622X-RAY DIFFRACTION98
2.371-2.4960.19221370.1622643X-RAY DIFFRACTION100
2.496-2.65240.17921370.15532674X-RAY DIFFRACTION100
2.6524-2.85720.20251260.1552699X-RAY DIFFRACTION100
2.8572-3.14460.18071690.16512626X-RAY DIFFRACTION100
3.1446-3.59950.17231390.15612714X-RAY DIFFRACTION100
3.5995-4.53440.16461340.14382731X-RAY DIFFRACTION100
4.5344-46.43530.21081550.1692850X-RAY DIFFRACTION100
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)
14.4981.5847-0.59393.09130.35441.9379-0.01910.07060.0407-0.010.01630.1103-0.0637-0.05890.02160.0770.03560.00220.06760.00330.0614-13.040724.0706-9.0656
23.10290.9841-0.50523.113-0.77841.00730.02210.06640.07080.0567-0.0044-0.0183-0.17210.1008-0.04260.104-0.0084-0.01280.0664-0.01920.06670.52223.2898-8.299
35.4913-2.4766-2.90163.78754.39977.31440.001-0.2742-0.16550.1177-0.01560.14440.2479-0.02320.02610.091-0.00480.00310.07320.00550.084-12.343514.285-4.0052
40.57821.97580.64227.25342.32240.75410.1185-0.0431-0.03410.7316-0.22490.54490.171-0.19290.16120.1415-0.03340.06890.166-0.02390.1912-23.415210.7442-2.0233
55.3259-0.6685-3.30282.44870.09677.1094-0.185-0.021-0.34850.1447-0.07610.16710.1609-0.15260.20850.08120.0001-0.00160.0758-0.04120.1281-16.33962.4834-11.3564
63.70013.6197-3.42377.5281-4.81214.9993-0.05030.09040.0446-0.0107-0.0746-0.4449-0.18670.0160.04740.1067-0.00140.00330.0945-0.020.1102-4.567916.7025-28.418
77.05594.2251-3.46315.0614-1.86283.2219-0.1560.2944-0.3238-0.25360.0344-0.15760.2217-0.10110.17270.12230.0181-0.02680.1182-0.03450.0895-14.07115.0095-29.4264
81.72151.8213-0.53952.85550.61971.7416-0.14130.00040.06020.0915-0.19110.4066-0.0005-0.4230.04520.0665-0.0062-0.0050.2023-0.06010.1923-26.05026.5376-14.6062
91.04920.3546-0.19720.6538-0.32612.5625-0.05910.10940.0672-0.1544-0.06690.142-0.1281-0.25840.12150.10560.0245-0.03070.1194-0.03170.1114-19.671713.8175-24.9099
108.79123.5062-3.52948.1506-2.4648.20660.08960.38361.2761-0.2604-0.33910.4099-1.1883-0.1915-0.02730.2770.0891-0.10090.19850.01410.2519-19.959825.5331-18.2627
111.97150.07781.55532.96160.39433.29520.06410.0256-0.189-0.0141-0.03870.2170.2224-0.1662-0.03020.1134-0.03260.02160.0858-0.02130.1478-10.4132-11.8424-11.8963
120.95341.14720.08221.8154-0.74211.38250.1176-0.16320.1080.4691-0.0920.1381-0.0466-0.151-0.02240.15420.00750.03850.1126-0.0060.0925-6.96983.2104-0.4316
130.8052-1.6132-1.84037.67295.81925.2175-0.0890.09-0.0794-0.32440.09750.14640.07860.1289-0.01040.13230.0147-0.02180.1316-0.03660.09666.1443-4.2777-23.4756
141.80890.3156-0.32562.92652.42086.1706-0.10590.2790.0205-0.37440.1561-0.1246-0.35350.1799-0.16230.1012-0.02530.00620.1023-0.02590.12710.96667.5646-15.9156
151.92330.2642-0.25641.49860.47691.5882-0.01370.0429-0.14440.12130.1161-0.22420.14160.1291-0.10410.09540.006-0.03990.072-0.01660.1259.09380.0188-5.7264
162.5727-0.0605-0.86534.1323.63688.4086-0.10530.0972-0.85810.25340.1358-0.27710.88770.3097-0.0510.19750.0186-0.06270.1423-0.00570.30125.1745-13.3462-5.3416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 90 )
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 130 )
7X-RAY DIFFRACTION7chain 'A' and (resid 131 through 154 )
8X-RAY DIFFRACTION8chain 'A' and (resid 155 through 164 )
9X-RAY DIFFRACTION9chain 'A' and (resid 165 through 201 )
10X-RAY DIFFRACTION10chain 'A' and (resid 202 through 214 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 66 )
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 106 )
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 130 )
14X-RAY DIFFRACTION14chain 'B' and (resid 131 through 153 )
15X-RAY DIFFRACTION15chain 'B' and (resid 154 through 201 )
16X-RAY DIFFRACTION16chain 'B' and (resid 202 through 214 )

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