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- PDB-4ri7: Crystal structure of poplar glutathione transferase F1 mutant SER... -

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Basic information

Entry
Database: PDB / ID: 4ri7
TitleCrystal structure of poplar glutathione transferase F1 mutant SER 13 CYS
ComponentsPhi class glutathione transferase GSTF1
KeywordsTRANSFERASE / glutathione transferase fold
Function / homology
Function and homology information


response to chemical / glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-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-transferases Phi, C-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
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsPegeot, H. / Mathiot, S. / Didierjean, C. / Rouhier, N.
CitationJournal: Front Plant Sci / Year: 2014
Title: The poplar Phi class glutathione transferase: expression, activity and structure of GSTF1.
Authors: Pegeot, H. / Koh, C.S. / Petre, B. / Mathiot, S. / Duplessis, S. / Hecker, A. / Didierjean, C. / Rouhier, N.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Phi class glutathione transferase GSTF1
B: Phi class glutathione transferase GSTF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3504
Polymers48,7362
Non-polymers6152
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-22 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.299, 60.649, 119.900
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 Phi class glutathione transferase GSTF1 / Glutathione transferase F1


Mass: 24367.797 Da / Num. of mol.: 2 / Mutation: S13C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Gene: POPTR_0002s01650g / Production host: Escherichia coli (E. coli) / References: UniProt: A9PHH6, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN SEQUENCE ARE DUE TO POLYMORPHISM (RESIDUES 33 AND 86).

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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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6.5
Details: 30% w/v PEG4000, 100 mM MES sodium, pH 6.5, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97969 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 1.798→59.95 Å / Num. all: 38287 / Num. obs: 36838 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.7
Reflection shellResolution: 1.798→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.1 / % possible all: 79

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Processing

Software
NameVersionClassification
Xnemodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RI6

4ri6


Resolution: 1.798→40.863 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 19.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 1853 5.03 %RANDOM
Rwork0.1505 ---
all0.1528 36817 --
obs0.1528 36817 96.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.798→40.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 40 458 3916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113570
X-RAY DIFFRACTIONf_angle_d1.3014840
X-RAY DIFFRACTIONf_dihedral_angle_d13.3271338
X-RAY DIFFRACTIONf_chiral_restr0.049535
X-RAY DIFFRACTIONf_plane_restr0.008623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.84670.28861100.22662008X-RAY DIFFRACTION73
1.8467-1.9010.28761080.21432309X-RAY DIFFRACTION83
1.901-1.96240.24331370.20052590X-RAY DIFFRACTION94
1.9624-2.03250.28351420.17742750X-RAY DIFFRACTION100
2.0325-2.11390.21711410.17392755X-RAY DIFFRACTION100
2.1139-2.21010.20541250.15112804X-RAY DIFFRACTION100
2.2101-2.32660.20981560.16332750X-RAY DIFFRACTION100
2.3266-2.47230.20381590.14162766X-RAY DIFFRACTION100
2.4723-2.66320.20771530.14682777X-RAY DIFFRACTION100
2.6632-2.93110.191610.14642799X-RAY DIFFRACTION100
2.9311-3.35510.17971470.13122812X-RAY DIFFRACTION100
3.3551-4.22640.15341480.11722855X-RAY DIFFRACTION100
4.2264-40.87360.15341660.1462989X-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)
11.046-0.26550.19580.71-0.08551.36520.07650.2013-0.0322-0.2525-0.0522-0.06860.0087-0.0207-0.02990.13640.03030.01910.121-0.01730.099424.7819-7.08710.1502
20.9633-0.4840.00511.80280.33680.6130.11290.21230.2236-0.5369-0.1242-0.0938-0.3551-0.08120.07870.49510.15750.05210.19960.03990.158815.11444.8682-7.6586
31.05-0.21920.06071.76360.17990.55820.06760.0783-0.0994-0.1254-0.0550.0633-0.0772-0.1561-0.03980.10130.03430.00540.1325-0.01970.095615.2449-6.75583.7206
41.7559-0.01050.3940.6636-0.75932.97350.07750.0488-0.1860.1077-0.0026-0.04760.21930.0943-0.04540.11880.0243-0.0120.0802-0.00830.158926.3425-17.041612.7722
51.04790.1235-0.39031.7967-0.37941.16080.07970.06790.1321-0.165-0.07320.0304-0.1163-0.0435-0.01760.10040.0114-0.0010.1196-0.00230.120823.3266.014614.405
61.9578-1.93130.93754.9825-1.82512.0171-0.0173-0.03980.20650.0149-0.00960.0289-0.1251-0.03360.0170.1162-0.02680.01380.1272-0.01380.15829.262311.794521.9897
71.13130.35550.11721.2327-0.13241.10230.0420.0390.05870.02050.0366-0.1174-0.09690.1027-0.06380.0885-0.01450.03410.11-0.01550.139334.99722.437416.3018
82.1762-1.01711.70331.3452-0.02723.91930.09580.3386-0.0415-0.2919-0.0318-0.2445-0.06180.26540.06120.13990.0080.07570.1868-0.03830.167135.6296-2.28951.2498
90.84120.10550.17620.686-0.07050.6054-0.0289-0.0912-0.02370.21930.02010.0695-0.0859-0.1390.01880.1450.01660.01340.11270.0040.08678.5214-2.472833.5463
102.7630.1717-0.58012.56430.87190.7575-0.0248-0.1013-0.00330.24650.094-0.0731-0.32040.1306-0.07050.1844-0.0278-0.030.1191-0.00880.101821.25634.83535.2039
111.15060.08560.23640.5991-0.19221.0966-0.0291-0.0272-0.1644-0.0731-0.0053-0.12260.089-0.01920.0190.0907-0.01140.0130.07720.00190.103912.4054-11.327625.0677
121.018-0.0946-0.26152.30530.90381.03240.0835-0.09090.0866-0.0179-0.0934-0.1198-0.09940.0265-0.01370.079-0.00730.00140.129-0.00940.07659.76316.025516.619
132.64272.47891.30316.64642.70063.0861-0.00330.14250.2079-0.2550.03280.0147-0.32770.1707-0.03370.1217-0.00950.02170.13040.0180.10144.048311.61768.5962
140.8518-0.2839-0.05511.20010.25510.8842-0.01250.1156-0.05160.0450.00420.1640.0302-0.0810.00250.0755-0.00790.0110.11230.00030.098-1.94543.062815.2784
152.216-0.08120.19471.95120.52333.9921-0.1975-0.1675-0.06010.52330.13710.2990.0224-0.26820.08070.17530.0350.05360.14430.03090.1247-3.16-0.338730.4546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 92 )
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 129 )
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 152 )
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 200 )
8X-RAY DIFFRACTION8chain 'A' and (resid 201 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 39 )
10X-RAY DIFFRACTION10chain 'B' and (resid 40 through 57 )
11X-RAY DIFFRACTION11chain 'B' and (resid 58 through 92 )
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 129 )
13X-RAY DIFFRACTION13chain 'B' and (resid 130 through 152 )
14X-RAY DIFFRACTION14chain 'B' and (resid 153 through 200 )
15X-RAY DIFFRACTION15chain 'B' and (resid 201 through 215 )

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