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

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Basic information

Entry
Database: PDB / ID: 3rpp
TitleCrystal structure of human kappa class glutathione transferase in apo form
ComponentsGlutathione S-transferase kappa 1
KeywordsTRANSFERASE / glutathione transferase / kappa GST / Trx domain / GSH binding / detoxification / apo form
Function / homology
Function and homology information


Glutathione conjugation / glutathione peroxidase activity / peroxisomal matrix / glutathione transferase / glutathione transferase activity / epithelial cell differentiation / glutathione metabolic process / Peroxisomal protein import / peroxisome / mitochondrial matrix ...Glutathione conjugation / glutathione peroxidase activity / peroxisomal matrix / glutathione transferase / glutathione transferase activity / epithelial cell differentiation / glutathione metabolic process / 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
Glutathione S-transferase kappa 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Jul 20, 2011Group: Structure summary
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)79,8003
Polymers79,8003
Non-polymers00
Water13,547752
1
A: Glutathione S-transferase kappa 1

A: Glutathione S-transferase kappa 1


Theoretical massNumber of molelcules
Total (without water)53,2002
Polymers53,2002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2410 Å2
ΔGint-6 kcal/mol
Surface area21130 Å2
MethodPISA
2
B: Glutathione S-transferase kappa 1
C: Glutathione S-transferase kappa 1


Theoretical massNumber of molelcules
Total (without water)53,2002
Polymers53,2002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-7 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.113, 84.290, 87.316
Angle α, β, γ (deg.)90.000, 122.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-280-

HOH

21A-590-

HOH

31B-501-

HOH

41B-604-

HOH

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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.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.85 Å3/Da / Density % sol: 56.89 % / Mosaicity: 0.436 °
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7
Details: 15% polyethylene glycol 3350, 0.2M Mg(NO3)2, pH 7.0, hanging drop, temperature 277K

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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: 82817 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Χ2: 1.086 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2Diffraction-ID% possible all
1.8-1.865.90.2354.982680.2350.4731100
1.86-1.946.20.19582570.62100
1.94-2.036.20.16482550.6493100
2.03-2.136.20.1482150.7694100
2.13-2.276.30.12382470.8875100
2.27-2.446.30.1182780.9536100
2.44-2.696.30.09882861.0937100
2.69-3.086.30.0982781.2388100
3.08-3.886.20.09183311.9079100
3.88-5060.09184022.271099.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.236 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8869 / SU ML: 0.2 / σ(F): 1.4 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 4142 5 %RANDOM
Rwork0.1524 ---
obs0.1545 82807 99.65 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.081 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 128.36 Å2 / Biso mean: 27.5197 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.7062 Å2-0 Å21.0043 Å2
2--0.4816 Å20 Å2
3---0.2246 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5159 0 0 752 5911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065291
X-RAY DIFFRACTIONf_angle_d0.9547166
X-RAY DIFFRACTIONf_chiral_restr0.067790
X-RAY DIFFRACTIONf_plane_restr0.004911
X-RAY DIFFRACTIONf_dihedral_angle_d13.3922010
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7998-1.86410.2423790.17237624800397
1.8641-1.93870.21524060.145478918297100
1.9387-2.02690.18984280.140178628290100
2.0269-2.13380.19644170.141678168233100
2.1338-2.26740.20533750.138678938268100
2.2674-2.44240.21074170.149178708287100
2.4424-2.6880.18314070.145179128319100
2.688-3.07660.20564650.154478458310100
3.0766-3.87480.19424370.158179408377100
3.8748-29.23990.17294110.159780128423100

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