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- PDB-2c3n: Human glutathione-S-transferase T1-1, apo form -

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Basic information

Entry
Database: PDB / ID: 2c3n
TitleHuman glutathione-S-transferase T1-1, 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
IODIDE ION / Glutathione S-transferase theta-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / 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 / 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,22019
Polymers113,3164
Non-polymers1,90415
Water12,953719
1
A: GLUTATHIONE S-TRANSFERASE THETA 1
B: GLUTATHIONE S-TRANSFERASE THETA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,67310
Polymers56,6582
Non-polymers1,0158
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)57,5469
Polymers56,6582
Non-polymers8887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)164.577, 110.986, 56.295
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(0.989335, 0.059624, -0.132895), (0.059391, -0.998218, -0.00572), (-0.133, -0.002234, -0.991114)-1.21499, 56.87276, 3.8162
2given(0.999901, 0.003222, 0.013721), (-0.000558, -0.963716, 0.266928), (0.014084, -0.266909, -0.963619)2.52695, 113.71851, 35.81305
3given(0.987188, 0.068953, -0.14389), (-0.104578, 0.960709, -0.257103), (0.120508, 0.268857, 0.955612)1.11238, 60.09205, 17.04786

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Components

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


Mass: 28329.084 Da / Num. of mol.: 4
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-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONJUGATES REDUCED GLUTATHIONE TO A WIDE NUMBER OF EXOGENOUS AND ENDOGENOUS HYDROPHOBIC ELECTROPHILES
Sequence details6XHIS TAG ADDED TO THE N-TERMINUS OF PROTEIN

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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: 2.16 Å3/Da / Density % sol: 42.68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOUR DIFFUSION TECHINQUE; 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350,200 MM MG(NO3)2, 200MM NAI, 2 MM DTT] WAS MIXED WITH 5 MICROLITRES OF PROTEIN SOLUTION (10 ...Details: HANGING DROP VAPOUR DIFFUSION TECHINQUE; 5 MICROLITRES OF RESERVOIR SOLUTION [35% (V/V) PEG 3350,200 MM MG(NO3)2, 200MM NAI, 2 MM DTT] WAS 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: ID14-1 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.51→30 Å / Num. obs: 161402 / % possible obs: 97.7 % / Observed criterion σ(I): 2.3 / Redundancy: 2.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.4
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.3 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LJR

1ljr


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.584 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL 6XHIS TAG AND THE FOLLOWING METHIONINE IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 8125 5 %RANDOM
Rwork0.214 ---
obs0.216 154151 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 15 719 8422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227952
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.97910822
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45323.623345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.871151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8951552
X-RAY DIFFRACTIONr_chiral_restr0.0920.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.24009
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.25547
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2561
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7851.54840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43627841
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40333399
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8084.52981
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 554
Rwork0.288 11010

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