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- PDB-2c3q: Human glutathione-S-transferase T1-1 W234R mutant, complex with S... -

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Basic information

Entry
Database: PDB / ID: 2c3q
TitleHuman glutathione-S-transferase T1-1 W234R mutant, complex with S- hexylglutathione
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
S-HEXYLGLUTATHIONE / IODIDE ION / Glutathione S-transferase theta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 11, 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 1.4Oct 9, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Other / Structure summary
Category: pdbx_database_status / pdbx_entity_instance_feature / pdbx_entry_details
Item: _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_ligand_of_interest
Revision 1.5Dec 13, 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 S-TRANSFERASE THETA 1
B: GLUTATHIONE S-TRANSFERASE THETA 1
C: GLUTATHIONE S-TRANSFERASE THETA 1
D: GLUTATHIONE S-TRANSFERASE THETA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,70439
Polymers113,2004
Non-polymers5,50435
Water7,368409
1
A: GLUTATHIONE S-TRANSFERASE THETA 1
B: GLUTATHIONE S-TRANSFERASE THETA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41620
Polymers56,6002
Non-polymers2,81518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: GLUTATHIONE S-TRANSFERASE THETA 1
D: GLUTATHIONE S-TRANSFERASE THETA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,28919
Polymers56,6002
Non-polymers2,68917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.499, 109.683, 171.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99587, 0.01001, 0.090233), (0.000128, -0.993747, 0.111656), (0.090787, 0.111206, 0.989642)8.84402, -50.31929, 2.41165
2given(0.997826, -0.056849, -0.033324), (-0.060603, -0.990263, -0.125328), (-0.025875, 0.127075, -0.991556)19.93327, -53.89019, -81.88764
3given(-0.996643, 0.07132, 0.04021), (0.058429, 0.963595, -0.260904), (-0.057353, -0.257679, -0.964527)31.40539, -5.7179, -91.38487

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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: Chemical
ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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 COORDINATES BELOW.
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.19 %
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, 200 MM NAI AND 2 MM DITHIOTHREITOL] WERE MIXED WITH 5 MICROLITRES OF PROTEIN ...Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE, 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350, 200 MM MG(NO3)2, 200 MM NAI 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), 1 MICROLITRE 100 MM CACL2 AND 1 MICROLITRE 20 MM S-HEXYLGLUTATHIONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 82135 / % possible obs: 90.5 % / Observed criterion σ(I): 2.3 / Redundancy: 1.8 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 82.5

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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 2C3N

2c3n


Resolution: 1.85→28.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.283 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4328 5 %RANDOM
Rwork0.223 ---
obs0.224 82135 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7676 0 135 409 8220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227964
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.99410816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6935952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95623.647340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.935151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5291552
X-RAY DIFFRACTIONr_chiral_restr0.0280.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025944
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1430.33876
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.55480
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.5733
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.344
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7281.54849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27827792
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20933397
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5644.53024
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 315
Rwork0.346 5714

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