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- PDB-4lmv: Crystal structure of glutathione transferase GSTFuA2 from Phanero... -

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Basic information

Entry
Database: PDB / ID: 4lmv
TitleCrystal structure of glutathione transferase GSTFuA2 from Phanerochaete chrysosporium
ComponentsGlutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / GST fold / glutathione transferase
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CITRATE ANION / Glutathione transferase
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.204 Å
AuthorsDidierjean, C. / Favier, F. / Prosper, P.
CitationJournal: Plos One / Year: 2013
Title: Diversification of fungal specific class a glutathione transferases in saprotrophic fungi.
Authors: Mathieu, Y. / Prosper, P. / Favier, F. / Harvengt, L. / Didierjean, C. / Jacquot, J.P. / Morel-Rouhier, M. / Gelhaye, E.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
B: Glutathione transferase
C: Glutathione transferase
D: Glutathione transferase
E: Glutathione transferase
F: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,91117
Polymers171,4816
Non-polymers1,43011
Water0
1
A: Glutathione transferase
B: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6576
Polymers57,1602
Non-polymers4964
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-12 kcal/mol
Surface area21580 Å2
MethodPISA
2
C: Glutathione transferase
D: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6576
Polymers57,1602
Non-polymers4964
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-12 kcal/mol
Surface area21510 Å2
MethodPISA
3
E: Glutathione transferase
F: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5985
Polymers57,1602
Non-polymers4373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-11 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.412, 202.466, 192.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 2:253 ) AND (NOT ELEMENT H)
211CHAIN B AND (RESSEQ 2:253 ) AND (NOT ELEMENT H)
311CHAIN C AND (RESSEQ 2:253 ) AND (NOT ELEMENT H)
411CHAIN D AND (RESSEQ 2:253 ) AND (NOT ELEMENT H)
511CHAIN E AND (RESSEQ 2:253 ) AND (NOT ELEMENT H)
611CHAIN F AND (RESSEQ 2:253 ) AND (NOT ELEMENT H)

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Components

#1: Protein
Glutathione transferase / Glutathione S-transferase


Mass: 28580.236 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: A0A067XG72*PLUS, glutathione transferase
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5.6
Details: 0.1 sodium citrate, 30% w/v PEG 4000, pH 5.6, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2012
RadiationMonochromator: SI 311 CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.204→48.957 Å / Num. all: 32711 / Num. obs: 32711 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 78.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20.7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 4.9 / Num. unique all: 4723 / % possible all: 100

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Processing

Software
NameVersionClassification
PROXIMA1data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G19

4g19


Resolution: 3.204→48.957 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1656 5.07 %RANDOM
Rwork0.1892 ---
all0.1924 32711 --
obs0.1924 32677 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.204→48.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 98 0 12242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01712585
X-RAY DIFFRACTIONf_angle_d1.53617079
X-RAY DIFFRACTIONf_dihedral_angle_d16.0914656
X-RAY DIFFRACTIONf_chiral_restr0.0761740
X-RAY DIFFRACTIONf_plane_restr0.0072213
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2024X-RAY DIFFRACTIONPOSITIONAL
12B2024X-RAY DIFFRACTIONPOSITIONAL0.101
13C2024X-RAY DIFFRACTIONPOSITIONAL0.102
14D2024X-RAY DIFFRACTIONPOSITIONAL0.096
15E2024X-RAY DIFFRACTIONPOSITIONAL0.09
16F2024X-RAY DIFFRACTIONPOSITIONAL0.097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2041-3.29830.2961370.23582542
3.2983-3.40480.33821330.23992561
3.4048-3.52640.31141230.24272564
3.5264-3.66760.32861490.22922542
3.6676-3.83440.31891080.21452582
3.8344-4.03650.24221310.19812592
4.0365-4.28920.251400.18182544
4.2892-4.62020.23661490.1692563
4.6202-5.08470.22161590.16652580
5.0847-5.81940.25551360.17362598
5.8194-7.32790.20721380.17992629
7.3279-48.96250.19711530.16142724

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