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- PDB-3rpn: Crystal structure of human kappa class glutathione transferase in... -

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Basic information

Entry
Database: PDB / ID: 3rpn
TitleCrystal structure of human kappa class glutathione transferase in complex with S-hexylglutathione
ComponentsGlutathione S-transferase kappa 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kappa GST / Trx domain / GSH binding / detoxification / GTX / glutathione transferase inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Glutathione conjugation / glutathione peroxidase activity / peroxisomal matrix / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / Peroxisomal protein import / peroxisome / mitochondrial matrix ...Glutathione conjugation / glutathione peroxidase activity / peroxisomal matrix / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / Peroxisomal protein import / peroxisome / mitochondrial matrix / mitochondrion / extracellular exosome / membrane / cytosol
Similarity search - Function
Glutathione S-transferase kappa / HCCA isomerase/glutathione S-transferase kappa / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-HEXYLGLUTATHIONE / Glutathione S-transferase kappa 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, B. / Peng, Y. / Zhang, T. / Ding, J.
CitationJournal: Biochem.J. / Year: 2011
Title: Crystal structures and kinetic studies of human Kappa class glutathione transferase provide insights into the catalytic mechanism.
Authors: Wang, B. / Peng, Y. / Zhang, T. / Ding, J.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Structure summary
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase kappa 1
B: Glutathione S-transferase kappa 1
C: Glutathione S-transferase kappa 1
D: Glutathione S-transferase kappa 1
E: Glutathione S-transferase kappa 1
F: Glutathione S-transferase kappa 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,95512
Polymers159,6006
Non-polymers2,3556
Water14,484804
1
A: Glutathione S-transferase kappa 1
D: Glutathione S-transferase kappa 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9854
Polymers53,2002
Non-polymers7852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-25 kcal/mol
Surface area18960 Å2
MethodPISA
2
B: Glutathione S-transferase kappa 1
E: Glutathione S-transferase kappa 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9854
Polymers53,2002
Non-polymers7852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-26 kcal/mol
Surface area18820 Å2
MethodPISA
3
C: Glutathione S-transferase kappa 1
F: Glutathione S-transferase kappa 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9854
Polymers53,2002
Non-polymers7852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-26 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.364, 199.821, 66.714
Angle α, β, γ (deg.)90.00, 116.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione S-transferase kappa 1 / GST 13-13 / GST class-kappa / GSTK1-1 / hGSTK1 / Glutathione S-transferase subunit 13


Mass: 26600.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTK1, HDCMD47P / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2Q3, glutathione transferase
#2: Chemical
ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.49 Å3/Da / Density % sol: 50.6 % / Mosaicity: 0.527 °
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7
Details: 20% polyethylene glycol 3350, 0.2M NaSCN, pH 7.0, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
51
61
71
81
91
101
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 122112 / % possible obs: 73.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.046 / Χ2: 1.128 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2Diffraction-ID% possible all
1.8-1.862.90.2792.796350.2790.645167.4
1.86-1.942.90.2295110.869266.5
1.94-2.032.80.13895840.72366.6
2.03-2.132.80.10794220.822465.6
2.13-2.272.70.07293600.801565.4
2.27-2.442.60.05895310.853666.4
2.44-2.692.40.06102071.341771.1
2.69-3.082.20.064116842.199881.3
3.08-3.882.40.044134661.813993.5
3.88-5030.03129551.2791089.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YZX

1yzx


Resolution: 1.9→29.951 Å / FOM work R set: 0.8341 / SU ML: 0.2 / σ(F): 0.55 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 5841 5.01 %random
Rwork0.1829 ---
obs0.1846 116630 95.54 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.755 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8439 Å20 Å20.4385 Å2
2--1.0066 Å2-0 Å2
3---0.8374 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10458 0 156 804 11418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710872
X-RAY DIFFRACTIONf_angle_d0.98914706
X-RAY DIFFRACTIONf_dihedral_angle_d13.724158
X-RAY DIFFRACTIONf_chiral_restr0.0671596
X-RAY DIFFRACTIONf_plane_restr0.0041878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.26555820.218611217X-RAY DIFFRACTION97
1.9679-2.04670.24555900.194911512X-RAY DIFFRACTION100
2.0467-2.13980.24256160.193911587X-RAY DIFFRACTION99
2.1398-2.25260.2316070.180611474X-RAY DIFFRACTION100
2.2526-2.39370.21055880.168411553X-RAY DIFFRACTION99
2.3937-2.57840.22186130.168711501X-RAY DIFFRACTION99
2.5784-2.83770.2246190.185211445X-RAY DIFFRACTION99
2.8377-3.24790.20825750.182811182X-RAY DIFFRACTION96
3.2479-4.09040.21085150.17289928X-RAY DIFFRACTION85
4.0904-29.95460.2065360.19069390X-RAY DIFFRACTION81
Refinement TLS params.Method: refined / Origin x: 5.9704 Å / Origin y: -33.6106 Å / Origin z: 24.7373 Å
111213212223313233
T0.1199 Å20.0229 Å2-0.0242 Å2-0.0998 Å2-0.0075 Å2--0.1025 Å2
L0.0475 °20.0053 °2-0.0303 °2-1.0038 °2-0.3327 °2--0.2013 °2
S0.0019 Å °0.0005 Å °-0.0026 Å °-0.1607 Å °0.0214 Å °0.1411 Å °0.0741 Å °0.0078 Å °-0.0227 Å °
Refinement TLS groupSelection details: all

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