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- PDB-1mtc: GLUTATHIONE TRANSFERASE MUTANT Y115F -

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Basic information

Entry
Database: PDB / ID: 1mtc
TitleGLUTATHIONE TRANSFERASE MUTANT Y115F
ComponentsGlutathione S-transferase YB1
KeywordsTRANSFERASE / GLUTATHIONE TRANSFERASE / PROTEIN DYNAMICS / PROTEIN CATALYSIS
Function / homology
Function and homology information


Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase ...Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / glutathione binding / response to metal ion / prostaglandin metabolic process / nickel cation binding / glutathione transferase / glutathione transferase activity / response to axon injury / response to amino acid / xenobiotic catabolic process / steroid binding / glutathione metabolic process / response to lead ion / sensory perception of smell / cellular response to xenobiotic stimulus / response to ethanol / response to xenobiotic stimulus / protein kinase binding / enzyme binding / protein homodimerization activity / protein-containing complex / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / 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. ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / : / 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
Chem-GPR / Glutathione S-transferase Mu 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLadner, J.E. / Xiao, G. / Armstrong, R.N. / Gilliland, G.L.
CitationJournal: Biochemistry / Year: 2002
Title: Local protein dynamics and catalysis: detection of segmental motion associated with rate-limiting product release by a glutathione transferase
Authors: Codreanu, S.G. / Ladner, J.E. / Xiao, G. / Stourman, N.V. / Hachey, D.L. / Gilliland, G.L. / Armstrong, R.N.
History
DepositionSep 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase YB1
B: Glutathione S-transferase YB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6094
Polymers51,6062
Non-polymers1,0032
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-25 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.750, 68.580, 80.460
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein Glutathione S-transferase YB1 / E.C.2.5.1.18 / Chain 3 / GST M1-1 / GST class-Mu 1 / glutathione S-transferase Yb-1 subunit


Mass: 25802.791 Da / Num. of mol.: 2 / Mutation: Y115F
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHROPHENANTHRENE
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: liver / Plasmid: pGT33MX / Production host: Escherichia coli (E. coli) / References: UniProt: P04905, glutathione transferase
#2: Chemical ChemComp-GPR / (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE


Mass: 501.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N3O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.88 Å3/Da / Density % sol: 45.03 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: ammonoium sulfate at pH 8.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Ji, X., (1992) Biochemistry, 31, 10169.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
225 mMTris1droppH8.0
31 mMEDTA1drop
40.2 %beta-D-glucopyranoside1drop
51 mMinhibitor1droppH8.
640-50 %satammonium sulfate1drop
760-72 %satammonium sulfate1reservoir
825 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 143 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Mar 25, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 21775 / % possible obs: 94 % / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 33
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 8 / % possible all: 91
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GST

3gst


Resolution: 2.2→10 Å / Num. parameters: 15571 / Num. restraintsaints: 15303 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
all0.2033 21775 --
obs-21775 94.6 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3889
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 70 185 3887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.039
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0151
X-RAY DIFFRACTIONs_zero_chiral_vol0.016
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS

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