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- PDB-6tum: Crystal structure of glutathione s-transferase PA1623 from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 6tum
TitleCrystal structure of glutathione s-transferase PA1623 from Pseudomonas aeruginosa PACS2 complexed with tartrate
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Glutathione-S-Transferase / Detoxification / Oxidoreductase / Nu-class
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Glutathione S-transferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsFeiler, C.G. / Blankenfeldt, W.
CitationJournal: To Be Published
Title: Crystal structure of glutathione s-transferase PA1623 from Pseudomonas aeruginosa PACS2 complexed with tartrate
Authors: Feiler, C.G. / Blankenfeldt, W.
History
DepositionJan 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9804
Polymers50,6792
Non-polymers3002
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-18 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.240, 96.728, 50.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-624-

HOH

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Components

#1: Protein Glutathione S-transferase /


Mass: 25339.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: yfcG_4, NCTC13628_04787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A485ICL5
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BisTris pH 6.5, 0.1 M sodium potassium tartrate, 22 % PEG 3350
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.48→43.62 Å / Num. obs: 72280 / % possible obs: 99.47 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.043 / Rrim(I) all: 0.088 / Net I/σ(I): 13.86
Reflection shellResolution: 1.48→1.533 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 7043 / CC1/2: 0.5 / Rpim(I) all: 0.86 / Rrim(I) all: 1.72 / % possible all: 98.15

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ECI

4eci


Resolution: 1.48→43.62 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.51
RfactorNum. reflection% reflection
Rfree0.204 2101 2.91 %
Rwork0.1604 --
obs0.1617 72256 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.42 Å2 / Biso mean: 25.7114 Å2 / Biso min: 10.89 Å2
Refinement stepCycle: final / Resolution: 1.48→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 28 424 3695
Biso mean--36.39 33.76 -
Num. residues----408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.510.35981340.35164459459396
1.51-1.550.32581380.30234627476599
1.55-1.590.32381380.26534622476099
1.59-1.640.30821380.23894614475299
1.64-1.690.2841400.210346534793100
1.69-1.750.23811380.196446394777100
1.75-1.820.26641400.193746674807100
1.82-1.910.27671400.181546704810100
1.91-2.010.23221400.156146784818100
2.01-2.130.17621400.137646784818100
2.13-2.30.17551400.128247094849100
2.3-2.530.18811400.130246854825100
2.53-2.90.17951420.138547464888100
2.9-3.650.18131440.140947944938100
3.65-43.620.16391490.14574970511999

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