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- PDB-1okt: X-ray Structure of Glutathione S-Transferase from the Malarial Pa... -

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Basic information

Entry
Database: PDB / ID: 1okt
TitleX-ray Structure of Glutathione S-Transferase from the Malarial Parasite Plasmodium falciparum
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GST / PLASMODIUM FALCIPARUM
Function / homology
Function and homology information


Heme degradation / Paracetamol ADME / Glutathione conjugation / 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 / 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 / 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 / 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
FORMIC ACID / Glutathione S-transferase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsFritz-Wolf, K. / Becker, A. / Rahlfs, s. / Harwaldt, P. / Schirmer, R.H. / Kabsch, W. / Becker, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: X-Ray Structure of Glutathione S-Transferase from the Malarial Parasite Plasmodium Falciparum
Authors: Fritz-Wolf, K. / Becker, A. / Rahlfs, S. / Harwaldt, P. / Schirmer, R.H. / Kabsch, W. / Becker, K.
History
DepositionJul 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8647
Polymers49,6342
Non-polymers2305
Water5,603311
1
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules

A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,72814
Polymers99,2684
Non-polymers46010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.360, 63.000, 75.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

21B-2008-

HOH

31B-2069-

HOH

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


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 M15 (bacteria) / References: UniProt: Q8MU52, glutathione transferase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.138 Å3/Da / Density % sol: 40 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 Msodium formate1drop
22.5 mMsodium phosphate1drop
315 mM1droppH7.8NaCl
44.3 mg/mlprotein1drop
53 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8045
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8045 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33867 / % possible obs: 98.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 98.8 % / Redundancy: 3.6 % / Mean I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→19.22 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1768668.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE FIRST THREE N-TERMINAL- RESIDUES AND RESIDUES 143-149 OF THE STRUCTURE ARE NOT WELL DEFINED BY THE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1017 3 %RANDOM
Rwork0.222 ---
obs0.222 33871 98.9 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.383249 e/Å3
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--8.65 Å20 Å2
3----6.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 15 311 3840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 167 3 %
Rwork0.305 5372 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FORMIAT.PARFORMIAT.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Num. reflection obs: 33823 / % reflection Rfree: 3 % / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67

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