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- PDB-1pa3: Crystal Structure of Glutathione-S-transferase from Plasmodium fa... -

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Basic information

Entry
Database: PDB / ID: 1pa3
TitleCrystal Structure of Glutathione-S-transferase from Plasmodium falciparum
ComponentsGlutathione s-transferase, putative
KeywordsTRANSFERASE
Function / homology
Function and homology information


Glutathione conjugation / Heme degradation / Paracetamol ADME / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Azathioprine ADME / Detoxification of Reactive Oxygen Species / Neutrophil degranulation / glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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
Glutathione S-transferase / Glutathione S-transferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 Å
AuthorsPerbandt, M. / Betzel, C. / Liebau, E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Native and inhibited structure of a Mu class-related glutathione S-transferase from Plasmodium falciparum
Authors: Perbandt, M. / Burmeister, C. / Walter, R.D. / Betzel, C. / Liebau, E.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione s-transferase, putative
B: Glutathione s-transferase, putative


Theoretical massNumber of molelcules
Total (without water)49,6342
Polymers49,6342
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-15 kcal/mol
Surface area20000 Å2
MethodPISA
2
A: Glutathione s-transferase, putative
B: Glutathione s-transferase, putative

A: Glutathione s-transferase, putative
B: Glutathione s-transferase, putative


Theoretical massNumber of molelcules
Total (without water)99,2684
Polymers99,2684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10880 Å2
ΔGint-53 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.1, 88.2, 75.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glutathione s-transferase, putative


Mass: 24817.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: Q95V54, UniProt: Q8MU52*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: Burmeister, C., (2003) Acta Cryst., D59, 1469.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
22.1 Mammonium sulfate1reservoir
30.1 Msodium cacodylate1reservoirpH6.0
42 mMglutathione1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13330 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.6 Å / % possible all: 97.92
Reflection
*PLUS
Num. obs: 13027 / % possible obs: 97.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.13
Reflection shell
*PLUS
Lowest resolution: 2.69 Å / % possible obs: 94.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.3

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Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28493 636 5% of total
Rwork0.22753 --
obs0.23032 11567 -
all-12286 -
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 0 32 3308
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Num. reflection Rfree: 658 / % reflection Rfree: 5 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / Rfactor Rwork: 0.322

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