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- PDB-7pka: Synechocystis sp. PCC6803 glutathione transferase Chi 1, GSOH bound -

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Basic information

Entry
Database: PDB / ID: 7pka
TitleSynechocystis sp. PCC6803 glutathione transferase Chi 1, GSOH bound
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Glutathione transferase / glutathione / cyanobacteria / chi class
Function / homology
Function and homology information


glutathione binding / glutathione transferase activity / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
S-Hydroxy-Glutathione / : / Glutathione S-transferase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsDidierjean, C. / Mocchetti, E. / Hecker, A. / Favier, F.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Structure and functions of glutathione transferase Chi 1 from cyanobacterium Synechocystis sp. PCC 6803
Authors: Mocchetti, E. / Hecker, A. / Mathiot, S. / Favier, F. / Cassier-Chauvat, C. / Chauvat, F. / Didierjean, C.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)43,6195
Polymers42,9332
Non-polymers6863
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-15 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.613, 92.613, 193.561
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glutathione S-transferase


Mass: 21466.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: gst / Production host: Escherichia coli (E. coli) / References: UniProt: Q55139
#2: Chemical ChemComp-GS8 / S-Hydroxy-Glutathione


Mass: 323.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O7S
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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

Crystal growTemperature: 277 K / Method: evaporation
Details: Protein solution: 44 mg/mL protein, 12 mM GSH, 30mM Tris pH 8, 200 mM NaCl; Reservoir solution: 16% (w/v) PEG 8000, 40 mM Potassium phosphate monobasic 2, 20% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980111 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980111 Å / Relative weight: 1
ReflectionResolution: 2.16→48.39 Å / Num. obs: 45994 / % possible obs: 99.7 % / Redundancy: 26.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.023 / Χ2: 0.96 / Net I/σ(I): 21.6
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 25.3 % / Rmerge(I) obs: 1.749 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3829 / CC1/2: 0.95 / Rpim(I) all: 0.343 / Χ2: 0.93 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSVERSION Jan 31, 2020data reduction
AimlessVersion 0.7.4data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LSZ

3lsz


Resolution: 2.16→31.47 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.157 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 2275 -RANDOM
Rwork0.2159 ---
obs0.2167 45898 99.7 %-
Displacement parametersBiso mean: 52.98 Å2
Baniso -1Baniso -2Baniso -3
1--12.1517 Å20 Å20 Å2
2---12.1517 Å20 Å2
3---24.3035 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.16→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 43 304 3209
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083068HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.954178HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1034SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it3068HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2716SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion15.31
LS refinement shellResolution: 2.16→2.18 Å
RfactorNum. reflection% reflection
Rfree0.3936 45 -
Rwork0.3247 --
obs0.328 918 90.24 %

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