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- PDB-6k93: Crystal structure of the type III effector XopAI from Xanthomonas... -

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Basic information

Entry
Database: PDB / ID: 6k93
TitleCrystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri in space group P41212
ComponentsType III effector XopAI
KeywordsCELL INVASION / type III effectors / peptide-binding domain / mono-ADP-ribosyltransferase fold / Xanthomonas axonopodis pv. citri
Function / homology
Function and homology information


cellular anatomical structure / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / nucleotidyltransferase activity
Similarity search - Function
NAD:arginine ADP-ribosyltransferase, ART / NAD:arginine ADP-ribosyltransferase / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NAD(+)--protein-arginine ADP-ribosyltransferase
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsLiu, J.-H. / Lai, Y.H. / Yang, J.-Y. / Hou, M.-H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)MOST 106-2313-B-005-029 Taiwan
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structure-Based Exploration of Arginine-Containing Peptide Binding in the ADP-Ribosyltransferase Domain of the Type III Effector XopAI Protein.
Authors: Liu, J.H. / Yang, J.Y. / Hsu, D.W. / Lai, Y.H. / Li, Y.P. / Tsai, Y.R. / Hou, M.H.
History
DepositionJun 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Type III effector XopAI


Theoretical massNumber of molelcules
Total (without water)35,8661
Polymers35,8661
Non-polymers00
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12960 Å2
Unit cell
Length a, b, c (Å)52.980, 52.980, 212.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-477-

HOH

31A-491-

HOH

41A-629-

HOH

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Components

#1: Protein Type III effector XopAI


Mass: 35866.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Strain: XW19 / Gene: XopAI, XAC3230 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL+ / References: UniProt: Q8PHM1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16.5% 7(V/V) PEG400, 6.5%(W/V) PEG 20000, 50mM KH2PO4, pH 8.0, 1 uL of 10 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9198 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.53→37.48 Å / Num. obs: 47011 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 14.597 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.041 / Rrim(I) all: 0.138 / Χ2: 0.91 / Net I/σ(I): 9.6
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.064 / Num. unique obs: 2290 / CC1/2: 0.647 / Rpim(I) all: 0.464 / Χ2: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMv7.2.2data reduction
pointlessv1.11.21data scaling
PHASERv2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eln

4eln
PDB Unreleased entry


Resolution: 1.53→36.891 Å / Cross valid method: FREE R-VALUE / Phase error: 16.04
RfactorNum. reflection% reflection
Rfree0.1707 2347 5.01 %
Rwork0.161 --
obs0.1614 46850 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.65 Å2
Refinement stepCycle: LAST / Resolution: 1.53→36.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 0 374 2347
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1749-0.1503-0.30981.29250.26280.3459-0.21650.25710.1357-0.29390.00580.318-0.4332-0.0335-0.20830.22-0.0346-0.04910.14680.02310.1063.837615.7335-40.6888
20.79350.52190.27160.62060.09731.0916-0.04340.13620.0533-0.22440.04910.1243-0.1996-0.2050.01980.13850.0201-0.02040.17180.00750.12198.015326.0059-28.3217
30.27130.12660.26950.76440.08630.14940.05620.0237-0.04640.06140.0159-0.01120.1488-0.05240.00010.1179-0.028-0.00250.1868-0.01280.14836.43457.8215-22.6167
40.21180.25820.32550.69510.16070.44180.0114-0.0537-0.01040.0473-0.0037-0.01330.002-0.0914-0.00590.07960.0026-0.0040.1732-0.00210.11138.19217.2257-17.2951
50.50610.0531-0.00960.969-0.14770.329-0.2630.396-0.0051-0.25740.1265-0.3756-0.18820.315-0.05320.1598-0.0568-0.00150.20070.01550.143320.799628.2144-28.7865
60.3370.29190.30140.38430.03450.191-0.0233-0.0190.0585-0.01140.01020.0621-0.1042-0.1073-0.00360.09120.0259-0.00180.1534-0.01080.116611.978124.8724-14.742
70.36880.0625-0.12560.1151-0.01380.1946-0.06710.05980.16760.11290.0503-0.2801-0.14540.1427-0.00580.1715-0.01810.01190.11890.00220.18330.522235.3192-17.6791
80.1833-0.0662-0.06340.7190.04370.9366-0.0523-0.04070.0524-0.01290.0497-0.0072-0.0178-0.063-00.10520.0058-0.00210.1144-0.00520.106521.486224.9357-10.6009
90.56270.06480.45130.94930.30411.7871-0.01760.0090.01420.00790.1157-0.1484-0.10690.03610.00220.12160.0089-0.00380.0922-0.02340.140924.891429.5233-10.1939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 58:74 )A58 - 74
2X-RAY DIFFRACTION2( CHAIN A AND RESID 75:112 )A75 - 112
3X-RAY DIFFRACTION3( CHAIN A AND RESID 113:136 )A113 - 136
4X-RAY DIFFRACTION4( CHAIN A AND RESID 137:161 )A137 - 161
5X-RAY DIFFRACTION5( CHAIN A AND RESID 162:173 )A162 - 173
6X-RAY DIFFRACTION6( CHAIN A AND RESID 174:204 )A174 - 204
7X-RAY DIFFRACTION7( CHAIN A AND RESID 205:219 )A205 - 219
8X-RAY DIFFRACTION8( CHAIN A AND RESID 220:258 )A220 - 258
9X-RAY DIFFRACTION9( CHAIN A AND RESID 259:296 )A259 - 296

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