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- PDB-5agy: CRYSTAL STRUCTURE OF A TAU CLASS GST MUTANT FROM GLYCINE -

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Basic information

Entry
Database: PDB / ID: 5agy
TitleCRYSTAL STRUCTURE OF A TAU CLASS GST MUTANT FROM GLYCINE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / BINDING SITE / CATALYTIC DOMAIN / ENZYME / INDUCTION / DETOXIFICATION / HERBICIDES / KINETICS / SITE-DIRECTED MUTAGENESIS / SOY BEANS / GLUTATHIONE TRANSFERASE / PROTEIN STABILITY / CATALYTIC MECHANISM / XENOBIOTIC BINDING / ALLOSTERISM
Function / homology
Function and homology information


response to chemical / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / 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 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 Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / 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 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
4-NITROPHENYL METHANETHIOL / S-(P-NITROBENZYL)GLUTATHIONE / PHOSPHATE ION / Tau class glutathione S-transferase / Glutathione S-transferase
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAxarli, I. / Muleta, A.W. / Vlachakis, D. / Kossida, S. / Kotzia, G. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
CitationJournal: Biochem.J. / Year: 2016
Title: Directed Evolution of Tau Class Glutathione Transferases Reveals a Site that Regulates Catalytic Efficiency and Masks Cooperativity.
Authors: Axarli, I. / Muleta, A.W. / Vlachakis, D. / Kossida, S. / Kotzia, G. / Maltezos, A. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionFeb 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6979
Polymers51,1112
Non-polymers1,5857
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-32 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.241, 77.602, 99.078
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 / / GMGSTU4-MUTANT


Mass: 25555.590 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GLYCINE MAX (soybean) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O49235, UniProt: I1MJ34*PLUS, glutathione transferase
#2: Chemical ChemComp-4NM / 4-NITROPHENYL METHANETHIOL


Mass: 170.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8NO2S
#3: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N4O8S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5
Details: PEG 4K 27.5%, NH4OAC 0.2 M, NAOAC 0.1 M, PH 5.0, 10 MM GTB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→19.79 Å / Num. obs: 48837 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.95 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.45 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYJ

1oyj


Resolution: 1.75→19.794 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1874 1999 4.1 %
Rwork0.1667 --
obs0.1675 48816 99.47 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.859 Å2 / ksol: 0.394 e/Å3
Refinement stepCycle: LAST / Resolution: 1.75→19.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 103 410 4098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144062
X-RAY DIFFRACTIONf_angle_d1.0025262
X-RAY DIFFRACTIONf_dihedral_angle_d12.9091525
X-RAY DIFFRACTIONf_chiral_restr0.068557
X-RAY DIFFRACTIONf_plane_restr0.004671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79370.30571380.24913230X-RAY DIFFRACTION98
1.7937-1.84220.2511410.22273287X-RAY DIFFRACTION99
1.8422-1.89640.23631400.20343308X-RAY DIFFRACTION99
1.8964-1.95750.24481400.18373299X-RAY DIFFRACTION100
1.9575-2.02740.20471420.17253310X-RAY DIFFRACTION100
2.0274-2.10850.20581420.16783309X-RAY DIFFRACTION99
2.1085-2.20440.19731410.16813315X-RAY DIFFRACTION100
2.2044-2.32040.21811430.16093336X-RAY DIFFRACTION100
2.3204-2.46550.17231420.15813335X-RAY DIFFRACTION100
2.4655-2.65550.16641430.16343356X-RAY DIFFRACTION100
2.6555-2.9220.19831440.16933370X-RAY DIFFRACTION100
2.922-3.3430.1861450.1723391X-RAY DIFFRACTION100
3.343-4.20520.17231450.14353406X-RAY DIFFRACTION100
4.2052-19.79540.15451530.16213565X-RAY DIFFRACTION100

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