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

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Basic information

Entry
Database: PDB / ID: 6kly
TitleCrystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri in space group P43212
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


NAD+-protein-arginine ADP-ribosyltransferase activity => GO:0106274 / : / cellular anatomical entity / 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 / NAD(+)--protein-arginine ADP-ribosyltransferase
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsLiu, J.-H. / Wu, J.E. / Lin, H. / Chiu, S.W. / Yang, J.Y.
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
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 21, 2019ID: 4ELN
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
Water4,252236
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 area12540 Å2
Unit cell
Length a, b, c (Å)73.050, 73.050, 114.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-407-

HOH

31A-409-

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, UniProt: A0A0U5GCU5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% (v/v) PEG 400, 5.5% (w/v) PEG 20000, 0.05 M Potassium phosphate, pH 8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11101N
21101N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13C110.9762
SYNCHROTRONNSRRC BL13B120.9056, 0.9193, 0.9190
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 19, 2010mirrors
ADSC QUANTUM 3152CCDJul 7, 2010mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.90561
30.91931
40.9191
ReflectionResolution: 2.01→28.35 Å / Num. obs: 19639 / % possible obs: 93.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.043 / Rrim(I) all: 0.094 / Χ2: 0.93 / Net I/σ(I): 11.1
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.525 / Num. unique obs: 1275 / CC1/2: 0.712 / Rpim(I) all: 0.29 / Rrim(I) all: 0.605 / Χ2: 0.91 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260: ???refinement
iMOSFLMv7.2.2data reduction
pointlessv1.11.21data scaling
PHENIX1.14_3260: ???phasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→26.563 Å / Cross valid method: FREE R-VALUE / Phase error: 17.92
RfactorNum. reflection% reflection
Rfree0.1949 952 5 %
Rwork0.1657 --
obs0.1671 19036 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.93 Å2
Refinement stepCycle: LAST / Resolution: 2.01→26.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 0 236 2197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0102-2.11610.22971200.22312249236980
2.1161-2.24860.21991250.19462388251385
2.2486-2.42210.23071270.17272520264789
2.4221-2.66570.21151470.1742571271891
2.6657-3.05090.19311500.16732653280393
3.0509-3.8420.19551530.15082774292795
3.842-26.56530.16221300.15282929305995
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)
11.1832-0.77520.07680.5408-0.04610.2738-0.06290.1621-0.1171-0.2590.08530.0089-0.5238-0.03690.00440.4036-0.1265-0.00140.2972-0.01120.1188-11.8683-29.8658-38.308
20.70660.16390.15470.92760.66160.6313-0.10620.1145-0.1246-0.23510.0850.1472-0.05450.0246-0.05120.1632-0.0281-0.0350.0911-0.01370.1189-12.9363-22.8574-26.5814
30.1014-0.06510.06210.86980.38180.5261-0.07460.0161-0.0029-0.15280.05220.0261-0.06590.07090.0040.1394-0.0311-0.01870.1232-0.00940.1143-10.4505-18.7898-21.4129
40.09810.1537-0.05290.4934-0.18470.2739-0.06590.0110.0278-0.12490.0210.0537-0.09260.0726-0.00220.1298-0.0108-0.01470.1182-0.00390.118-7.1477-11.3003-17.4241
50.20290.1076-0.23270.20730.03610.52570.0174-0.04670.0261-0.0745-0.04950.0285-0.04530.09110.00150.1241-0.0124-0.01630.09230.01290.1063-5.086-9.2718-10.8328
60.24380.1806-0.33040.65060.00740.5510.0075-0.0438-0.01620.0518-0.0195-0.118-0.01790.11170.02110.1451-0.0249-0.02790.12240.0170.1338-1.755-4.9298-10.2412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 60:74 )A60 - 74
2X-RAY DIFFRACTION2( CHAIN A AND RESID 75:136 )A75 - 136
3X-RAY DIFFRACTION3( CHAIN A AND RESID 137:173 )A137 - 173
4X-RAY DIFFRACTION4( CHAIN A AND RESID 174:214 )A174 - 214
5X-RAY DIFFRACTION5( CHAIN A AND RESID 215:260 )A215 - 260
6X-RAY DIFFRACTION6( CHAIN A AND RESID 261:296 )A261 - 296

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