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- PDB-1r4w: Crystal structure of Mitochondrial class kappa glutathione transferase -

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Basic information

Entry
Database: PDB / ID: 1r4w
TitleCrystal structure of Mitochondrial class kappa glutathione transferase
ComponentsGlutathione S-transferase, mitochondrial
KeywordsTRANSFERASE / glutathione-S-transferase / glutathione transferase / kappa GST / rGSTK1-1
Function / homology
Function and homology information


Glutathione conjugation / Peroxisomal protein import / glutathione peroxidase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / epithelial cell differentiation / peroxisome / mitochondrial matrix / mitochondrion
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 / Glutathione S-transferase kappa 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR with anomalous Hg / Resolution: 2.5 Å
AuthorsLadner, J.E. / Parsons, J.F. / Rife, C.L. / Gilliland, G.L. / Armstrong, R.N.
CitationJournal: Biochemistry / Year: 2004
Title: Parallel Evolutionary Pathways for Glutathione Transferases: Structure and Mechanism of the Mitochondrial Class Kappa Enzyme rGSTK1-1
Authors: Ladner, J.E. / Parsons, J.F. / Rife, C.L. / Gilliland, G.L. / Armstrong, R.N.
History
DepositionOct 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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, mitochondrial
B: Glutathione S-transferase, mitochondrial
C: Glutathione S-transferase, mitochondrial
D: Glutathione S-transferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3298
Polymers102,1004
Non-polymers1,2294
Water4,792266
1
A: Glutathione S-transferase, mitochondrial
B: Glutathione S-transferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6654
Polymers51,0502
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-29 kcal/mol
Surface area18420 Å2
MethodPISA
2
C: Glutathione S-transferase, mitochondrial
D: Glutathione S-transferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6654
Polymers51,0502
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-25 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.900, 110.790, 74.740
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutathione S-transferase, mitochondrial / / GST 13-13 / Glutathione S-transferase subunit 13 / GST class-kappa


Mass: 25524.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GSGSTK1-1 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P24473, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHOH 723 MAY BE A PARTIALLY OCCUPIED SULFATE ION.

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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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: well: 13-17% (w/v) PEG 2K, 40-80 mM lithium sulfate, 100 mM sodium citrate; drop: 1:1 protein:well, 0.05% beta-octyl-glucopyranoside, 1.5 mM glutathione, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 4.4 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
20.2 %beta-n-octylglucopyranoside1drop
33-5 mMligands1drop
40.1 M1dropLiSO4
57 %PEG30001dropor PEG6000, pH4.0-4.4
650 mMsodium citrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 35795 / Num. obs: 35795 / % possible obs: 98.4 % / Redundancy: 4 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.072 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 115187 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 88.7 % / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1refinement
RESOLVEphasing
RefinementMethod to determine structure: SIR with anomalous Hg / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 --random
Rwork0.204 ---
all-66183 --
obs-62942 92.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6996 0 80 266 7342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg1.82
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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