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- PDB-2c3t: Human glutathione-S-transferase T1-1, W234R mutant, apo form -

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Basic information

Entry
Database: PDB / ID: 2c3t
TitleHuman glutathione-S-transferase T1-1, W234R mutant, apo form
ComponentsGLUTATHIONE S-TRANSFERASE THETA 1
KeywordsTRANSFERASE / GLUTATHIONE / GLUTATHIONE TRANSFERASE / T1-1 / POLYMORPHISM
Function / homology
Function and homology information


Glutathione conjugation / Paracetamol ADME / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase Theta, N-terminal / Glutathione S-transferase Theta, C-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 ...Glutathione S-transferase Theta, N-terminal / Glutathione S-transferase Theta, C-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-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 S-transferase theta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTars, K. / Larsson, A.-K. / Shokeer, A. / Olin, B. / Mannervik, B. / Kleywegt, G.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of the Suppressed Catalytic Activity of Wild-Type Human Glutathione Transferase T1-1 Compared to its W234R Mutant.
Authors: Tars, K. / Larsson, A.-K. / Shokeer, A. / Olin, B. / Mannervik, B. / Kleywegt, G.J.
History
DepositionOct 12, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE THETA 1
B: GLUTATHIONE S-TRANSFERASE THETA 1
C: GLUTATHIONE S-TRANSFERASE THETA 1
D: GLUTATHIONE S-TRANSFERASE THETA 1


Theoretical massNumber of molelcules
Total (without water)113,2004
Polymers113,2004
Non-polymers00
Water4,810267
1
A: GLUTATHIONE S-TRANSFERASE THETA 1
B: GLUTATHIONE S-TRANSFERASE THETA 1


Theoretical massNumber of molelcules
Total (without water)56,6002
Polymers56,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GLUTATHIONE S-TRANSFERASE THETA 1
D: GLUTATHIONE S-TRANSFERASE THETA 1


Theoretical massNumber of molelcules
Total (without water)56,6002
Polymers56,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)164.524, 111.822, 55.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.968587, -0.18315, -0.168211), (-0.183345, -0.982942, 0.014507), (-0.167998, 0.01679, -0.985644)9.99224, 54.59685, 57.82712
2given(-0.979651, 0.132596, 0.150673), (0.090234, 0.961524, -0.259478), (-0.179281, -0.240602, -0.953923)159.11601, 7.8967, 91.50109
3given(-0.998501, 0.05162, 0.018206), (-0.0453, -0.966004, 0.254527), (0.030725, 0.253321, 0.966894)165.27914, 46.28961, 21.41075

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE THETA 1 / HUMAN GLUTATHIONE TRANSFERASE T1-1 / GST CLASS-THETA 1


Mass: 28300.068 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P30711, glutathione transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TRP 233 TO ARG ENGINEERED RESIDUE IN CHAIN B, TRP 233 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, TRP 233 TO ARG ENGINEERED RESIDUE IN CHAIN B, TRP 233 TO ARG ENGINEERED RESIDUE IN CHAIN C, TRP 233 TO ARG ENGINEERED RESIDUE IN CHAIN D, TRP 233 TO ARG THE ENGINEERED RESIDUE IS NUMBERED 234 IN THE COORDINATE RECORDS BELOW.
Sequence details6XHIS TAG ADDED TO THE N-TERMINUS OF PROTEIN. RESIDUE TRP 234 MUTATED TO ARGININE.

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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: 2.31 Å3/Da / Density % sol: 46.41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE. 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350, 200 MM MG(NO3)2, AND 2 MM DITHIOTHREITOL] WERE MIXED WITH 5 MICROLITRES OF PROTEIN SOLUTION ...Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE. 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350, 200 MM MG(NO3)2, AND 2 MM DITHIOTHREITOL] WERE MIXED WITH 5 MICROLITRES OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8, 15 % GLYCEROL) AND 1 MICROLITRE OF 100 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.96
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 33761 / % possible obs: 86.5 % / Observed criterion σ(I): 2.3 / Redundancy: 1.5 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C3Q

2c3q


Resolution: 2.4→28.36 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.042 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 1.099 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1805 5.1 %RANDOM
Rwork0.213 ---
obs0.216 33761 86.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7676 0 0 267 7943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.98310696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2735952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.61223.647340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.831151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.6761552
X-RAY DIFFRACTIONr_chiral_restr0.0040.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.33938
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.55379
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5538
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.363
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8111.55028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3727792
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99333322
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0984.52904
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 123
Rwork0.273 2519

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