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- PDB-6nxv: Crystal structure of the theta class glutathione S-transferase fr... -

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Basic information

Entry
Database: PDB / ID: 6nxv
TitleCrystal structure of the theta class glutathione S-transferase from the citrus canker pathogen Xanthomonas axonopodis pv. citri, apo form
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / theta class GST / glutathione S-transferase / citrus canker / plant pathogen / dehalogenase
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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 ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
Glutathione S-transferase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsHilario, E. / De Keyser, S. / Fan, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)CA-R-BCH-5051-H United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural and biochemical characterization of a glutathione transferase from the citrus canker pathogen Xanthomonas.
Authors: Hilario, E. / De Keyser, S. / Fan, L.
History
DepositionFeb 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,56732
Polymers91,4044
Non-polymers1,16328
Water4,414245
1
A: Glutathione S-transferase
hetero molecules


  • defined by author
  • Evidence: gel filtration, The molecular mass of XacGST protein was determined by SDS-PAGE gels showing the apparent molecular mass around 23 kDa. The quaternary structure of XacGST was estimated by ...Evidence: gel filtration, The molecular mass of XacGST protein was determined by SDS-PAGE gels showing the apparent molecular mass around 23 kDa. The quaternary structure of XacGST was estimated by size exclusion chromatography using a HiPrep 16/60 Sephacryl S-100 HR column. XacGST was eluted at an elution volume of 58 mL, which corresponds to a molecular mass about 23 kDa (monomeric) when compared with the molecular weight markers used to calibrate the same column at same flowrate and temperature.
  • 23.1 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)23,0647
Polymers22,8511
Non-polymers2136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0716
Polymers22,8511
Non-polymers2205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,33311
Polymers22,8511
Non-polymers48310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0998
Polymers22,8511
Non-polymers2487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.159, 105.500, 124.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutathione S-transferase /


Mass: 22850.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: gst, XAC3819 / Plasmid: pETSUMO / Details (production host): pETSUMO-XAC3819 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLys-S / References: UniProt: Q8PG02
#2: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.66 % / Description: Needle-like crystal
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.1M Bis-Tris, pH 7.1, 0.2M magnesium chloride, 26% PEG 3,350. Crystals appear in 2-3 days and grow up to 6-7 days
PH range: 7.0 - 7.25 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cobra CryoSystem / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 9, 2018 / Details: Varimax Confocal Max-Flux
RadiationMonochromator: Osmic Varimax HF ArcSec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→80.439 Å / Num. all: 30033 / Num. obs: 30033 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Rsym value: 0.121 / Net I/av σ(I): 5.9 / Net I/σ(I): 8.9 / Num. measured all: 159325
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.9-305.30.1218.9300330.9940.0630.14898.6
2.75-2.95.40.686242820.7520.3560.84297.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.9 Å29.81 Å
Translation3.9 Å29.81 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 29943
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
11.04-10025.30.899502
8.74-11.0431.20.942510
7.54-8.7432.70.921556
6.73-7.54360.887623
6.13-6.7331.40.889679
5.67-6.1330.60.894737
5.3-5.6727.20.907790
4.99-5.324.80.914840
4.73-4.9922.90.91870
4.51-4.7321.30.904928
4.32-4.5119.30.923959
4.15-4.32210.913991
4-4.15220.9051035
3.86-420.10.9051075
3.74-3.8618.70.9061105
3.62-3.7419.90.9091117
3.52-3.6220.30.8991195
3.43-3.5222.60.891198
3.34-3.43220.8951224
3.26-3.3422.70.8841263
3.18-3.2622.40.8821280
3.11-3.18220.8941314
3.05-3.1125.90.8771370
2.99-3.0523.80.881337
2.93-2.9927.60.8651415
2.87-2.93280.8551419
2.82-2.8731.70.8241429
2.75-2.8235.70.8072182

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALA3.3.22data scaling
PHASER2.8.2phasing
DM7.0.068phasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NV6

6nv6


Resolution: 2.75→29.813 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2413 1444 4.82 %
Rwork0.1937 --
obs0.196 29941 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.1 Å2 / Biso mean: 47.9007 Å2 / Biso min: 23.7 Å2
Refinement stepCycle: final / Resolution: 2.75→29.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5798 0 41 262 6101
Biso mean--77.89 49.07 -
Num. residues----760
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.84820.34351430.26652788293198
2.8482-2.96220.3021410.24072781292298
2.9622-3.09690.28411500.22862799294998
3.0969-3.25990.28641430.2072802294598
3.2599-3.46390.26791330.1952826295998
3.4639-3.73090.23021460.17532827297399
3.7309-4.10550.2151570.16232843300098
4.1055-4.69760.2111400.16212857299799
4.6976-5.91090.20841550.19122914306999
5.9109-29.81490.24891360.21423060319699

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