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- PDB-6nv6: Crystal structure of the theta class glutathione S-transferase fr... -

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Basic information

Entry
Database: PDB / ID: 6nv6
TitleCrystal structure of the theta class glutathione S-transferase from the citrus canker pathogen Xanthomonas axonopodis pv. citri with glutathione bound
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 / Glutathione S-transferase
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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 4, 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 / 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
C: Glutathione S-transferase
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,41353
Polymers91,4044
Non-polymers2,00949
Water6,828379
1
A: Glutathione S-transferase
hetero molecules


  • defined by author
  • Evidence: gel filtration, To verify the oligomeric size of XacGST (Xac3819) in buffered solution, we have used a HiPrep 16/60 Sephacryl S-100 High Resolution column (GE Healthcare) equilibrated in ...Evidence: gel filtration, To verify the oligomeric size of XacGST (Xac3819) in buffered solution, we have used a HiPrep 16/60 Sephacryl S-100 High Resolution column (GE Healthcare) equilibrated in 25mM tris:HCl, pH 8.0, 300mM sodium chloride, 5% glycerol at 277K. 1mg of pure XacGST and control SjGST26 were loaded, independently, at a flowrate of 30mL/h and 2mL fraction size. While control SjGST26 showed to be a dimer, XacGST (Xac3819) showed to be a monomer. Marker proteins were used for column calibration: ferritin (440 kDa), aldolase (158 kDa), conalbumin (75 kDa), and lactalbumin (14 kDa).
  • 23.2 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)23,20511
Polymers22,8511
Non-polymers35510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,65516
Polymers22,8511
Non-polymers80415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,38316
Polymers22,8511
Non-polymers53215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,17010
Polymers22,8511
Non-polymers3199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.120, 106.510, 125.230
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: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8PG02, glutathione transferase
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 3.25 Å3/Da / Density % sol: 62.17 % / Description: Needle-like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 0.1M bis-tris:HCl, pH 7.0, 0.2M magnesium chloride and 25% (w/v) PEG 3,350
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: Sep 2, 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: 2.65→30 Å / Num. obs: 35328 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 25.263 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.063 / Rrim(I) all: 0.138 / Net I/av σ(I): 10.7 / Net I/σ(I): 10.7
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2 / Num. unique obs: 5096 / CC1/2: 0.632 / Rpim(I) all: 0.496 / Rrim(I) all: 0.812 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.44 Å30 Å
Translation7.44 Å30 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
iMOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KH7

4kh7


Resolution: 2.65→29.998 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.4
RfactorNum. reflection% reflection
Rfree0.2259 1999 5.67 %
Rwork0.1769 --
obs0.1798 35261 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.08 Å2 / Biso mean: 45.0081 Å2 / Biso min: 14.92 Å2
Refinement stepCycle: final / Resolution: 2.65→29.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6022 0 72 397 6491
Biso mean--64.12 44.92 -
Num. residues----778
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.65-2.71630.32791400.268223392479
2.7163-2.78960.35211410.252923412482
2.7896-2.87170.34581400.236523312471
2.8717-2.96430.30511420.243723542496
2.9643-3.07010.31861410.224923452486
3.0701-3.19290.25891410.205723392480
3.1929-3.33810.24891410.182723572498
3.3381-3.51380.23161420.181523542496
3.5138-3.73360.22741430.167523832526
3.7336-4.02120.19461420.142823572499
4.0212-4.42470.17891440.126723942538
4.4247-5.06240.16611450.131923992544
5.0624-6.3680.19571450.170624322577
6.368-29.99950.20071520.189425372689

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