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- PDB-6k94: Crystal structure of the type III effector XopAI from Xanthomonas... -

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Basic information

Entry
Database: PDB / ID: 6k94
TitleCrystal structure of the type III effector XopAI from Xanthomonas axonopodis pv. citri - a 70 residue N-terminal truncation
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: 2.26 Å
AuthorsLiu, J.-H. / Li, Y.-P. / 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
B: Type III effector XopAI
C: Type III effector XopAI
D: Type III effector XopAI


Theoretical massNumber of molelcules
Total (without water)115,8454
Polymers115,8454
Non-polymers00
Water10,052558
1
A: Type III effector XopAI


Theoretical massNumber of molelcules
Total (without water)28,9611
Polymers28,9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type III effector XopAI


Theoretical massNumber of molelcules
Total (without water)28,9611
Polymers28,9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Type III effector XopAI


Theoretical massNumber of molelcules
Total (without water)28,9611
Polymers28,9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Type III effector XopAI


Theoretical massNumber of molelcules
Total (without water)28,9611
Polymers28,9611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.780, 98.760, 77.450
Angle α, β, γ (deg.)90.000, 91.210, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Type III effector XopAI


Mass: 28961.355 Da / Num. of mol.: 4 / Fragment: 70 residue N-terminal truncation
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.: 558 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 10% (v/v) 2-propanol, 20% (w/v) PEG400, and 100 mM HEPES-NaOH, pH 9.5

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.26→31.53 Å / Num. obs: 44030 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.919 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.088 / Rrim(I) all: 0.167 / Χ2: 0.89 / Net I/σ(I): 7.5
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.783 / Num. unique obs: 4034 / CC1/2: 0.609 / Rpim(I) all: 0.482 / Rrim(I) all: 0.922 / Χ2: 0.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
iMOSFLMv7.2.2data reduction
pointlessv1.11.21data scaling
PHASERv2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4eln

4eln
PDB Unreleased entry


Resolution: 2.26→31.527 Å / Cross valid method: FREE R-VALUE / Phase error: 23.55
RfactorNum. reflection% reflection
Rfree0.2319 2222 5.05 %
Rwork0.1893 --
obs0.1915 44004 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.06 Å2
Refinement stepCycle: LAST / Resolution: 2.26→31.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7354 0 0 558 7912
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)
10.09450.0061-0.01040.03920.03140.0225-0.0324-0.2231-0.02760.014-0.10710.2311-0.0687-0.0422-0.00470.21260.0334-0.01890.2831-0.0790.2302-3.32796.256810.4381
20.02340.02770.0060.04130.0320.04190.0102-0.018-0.02860.0048-0.02190.0004-0.1891-0.0747-0.00010.19520.0039-0.02190.23280.00160.1906-0.60640.9993-4.4036
30.0853-0.1072-0.11270.12410.12350.1612-0.05220.1181-0.01540.03870.05930.0084-0-0.032500.1853-0.0065-0.01350.1986-0.0250.16087.5341-5.4732-6.8118
40.111-0.0509-0.11650.08670.15690.22340.0061-0.06530.0612-0.0453-0.07510.04360.0453-0.0187-0.00030.14860.0023-0.01410.15020.00150.17688.92461.0877.042
50.00880.02880.01460.1133-0.00710.0635-0.0847-0.0203-0.0145-0.032-0.00220.1716-0.09750.1022-00.1661-0.0001-0.00430.1503-0.00680.171615.49839.644316.1891
60.4604-0.0932-0.11670.01720.02510.033-0.0380.0171-0.18530.0383-0.0619-0.0356-0.2080.2497-0.01760.2188-0.0434-0.03320.28880.01670.139725.3711.325110.3625
70.13630.0205-0.03720.0076-0.03630.1594-0.0054-0.0083-0.0952-0.008-0.0781-0.0394-0.0585-0.0465-0.02970.12790.0163-0.0120.1423-0.01290.181216.9655-2.255710.4677
80.146-0.1628-0.08670.17570.09850.0569-0.1733-0.060.00320.25430.0924-0.0104-0.153-0.0488-0.02920.267-0.0631-0.07250.24530.01520.197224.11786.496217.8254
90.0694-0.0396-0.02890.1044-0.07820.0984-0.0293-0.002-0.15610.03690.06450.2503-0.0304-0.03230.00070.1694-0.00530.02180.2004-0.00470.35493.709430.0549-8.8504
100.07180.00340.04380.1187-0.03620.0461-0.02980.036-0.1770.13980.0003-0.08550.0151-0.0230.01340.1903-0.0260.04050.1422-0.0150.348613.724917.9918-7.9504
110.3975-0.1911-0.14170.2428-0.14190.3455-0.3248-0.0233-0.20850.0209-0.1063-0.05460.16880.0101-0.86670.21790.16280.18340.0840.04620.415125.189713.6591-8.6981
120.30540.0778-0.20850.2654-0.05480.1234-0.00570.0759-0.02930.0325-0.02190.0421-0.00770.0078-00.14050.0098-0.00910.1391-0.00660.182318.414333.105-11.3053
130.07040.06110.01570.0490.02790.01410.16320.07990.0324-0.010.0849-0.0561-0.00150.11240.00150.22750.01910.03290.2173-0.0020.21329.795941.6034-17.4469
140.06130.05440.02660.04670.02380.1337-0.0998-0.1358-0.0036-0.05150.1373-0.0391-0.02890.0443-0.04040.14760.02910.03680.25620.05260.222728.201931.3325-6.195
150.01870.02410.04780.02360.05070.1197-0.01050.06090.07580.112-0.0104-0.0203-0.04270.0965-0.00010.15380.00410.01160.19210.03140.225222.316541.6015-11.6786
160.40870.22120.19860.12650.10940.09890.1984-0.0274-0.0828-0.1216-0.1104-0.04420.0671-0.05650.00080.27790.06720.10660.17340.05760.312322.732748.353-18.7109
171.10020.3075-0.05530.088-0.01950.00420.0671-0.32480.07310.0538-0.1951-0.16440.07910.4225-0.10220.28480.0329-0.0550.51440.23710.277632.7186-23.6927-26.1338
180.03090.0509-0.0190.0692-0.04370.0604-0.1103-0.17730.0686-0.1566-0.2931-0.07130.13220.104600.24850.06280.04450.34790.09470.359330.7235-17.8019-40.7232
190.08680.06450.01050.07970.03740.1129-0.17820.0780.0063-0.0293-0.06410.1134-0.03770.0621-0.01160.3115-0.01050.03220.27780.0480.258623.1213-12.5593-48.9678
200.1809-0.127-0.06120.1042-0.00720.2134-0.1299-0.0563-0.02150.0171-0.06770.13690.09570.218-0.06230.1685-0.0369-0.01390.19970.04030.154721.0662-11.5714-37.8263
210.05080.04690.09830.2626-0.03770.44950.11890.00970.05070.0886-0.13130.06870.10220.1881-0.03020.24650.02290.01280.23390.04220.152818.7209-21.8758-29.5761
220.06330.07510.00030.0780.02120.12390.0467-0.0012-0.03180.05330.0379-0.0410.00510.07720.07710.22370.0270.02250.19460.0180.108615.2416-27.0478-21.0504
230.0246-0.0266-0.01770.03260.01590.0119-0.11610.10870.09170.03980.0865-0.05930.1435-0.1128-00.2953-0.03050.01840.2523-0.04870.17473.4266-21.7788-28.622
240.0360.0105-0.04570.07590.05010.0946-0.05790.0529-0.01020.04830.01350.1337-0.18190.140500.2418-0.01080.00970.23410.03790.192913.3345-13.5881-32.1968
250.0139-0.0120.00230.0104-0.00390.01720.01780.02420.01930.1141-0.0871-0.04930.0239-0.107100.3502-0.03180.02020.32810.04860.28768.3696-26.3624-16.1242
260.01020.0034-0.01690.0157-0.02960.0625-0.08040.0649-0.20250.14080.1047-0.0476-0.092-0.059300.2846-0.075-0.02040.29160.01360.24334.4803-27.7536-21.5534
270.09630.0169-0.02020.0825-0.07670.0753-0.1659-0.05770.1521-0.22920.24450.3028-0.0328-0.004-0.00150.2245-0.1037-0.06730.45490.09070.4252-291.1356-27.5043
280.49530.1591-0.57390.7089-0.55490.8747-0.0813-0.0820.4564-0.18590.25840.00760.23520.00220.07510.1810.0144-0.10820.18280.00470.4908-11.608614.3442-30.8908
290.68750.0774-0.02860.0825-0.02920.268-0.1059-0.18270.2403-0.18720.16650.11250.2025-0.0566-0.1150.2068-0.0292-0.07630.2110.04070.2119-12.95210.2226-28.2832
300.11190.0233-0.04780.11760.01130.0302-0.2011-0.14480.0499-0.1203-0.0123-0.00120.0466-0.0237-0.01960.1451-0.0176-0.01460.37910.01580.1658-14.2247-12.0221-21.0176
310.0622-0.0548-0.02720.07010.04780.04090.0992-0.0321-0.3108-0.0187-0.1848-0.1281-0.05390.0104-0.00030.2359-0.0838-0.04630.26380.04810.2114-4.8536-12.8611-19.9513
320.0647-0.0604-0.0240.0615-0.00760.077-0.0309-0.1120.0846-0.13030.03970.010.09710.0183-0.00010.2642-0.0131-0.00370.27350.02350.2184-6.867-3.5152-30.6821
33-0.0031-0.00160.00670.0581-0.03720.0160.061-0.0269-0.12060.1107-0.018-0.02130.0672-0.0972-00.3037-0.0853-0.03610.30160.06610.2373-10.94-19.7401-19.4643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 73:92 )A73 - 92
2X-RAY DIFFRACTION2( CHAIN A AND RESID 93:112 )A93 - 112
3X-RAY DIFFRACTION3( CHAIN A AND RESID 113:161 )A113 - 161
4X-RAY DIFFRACTION4( CHAIN A AND RESID 162:204 )A162 - 204
5X-RAY DIFFRACTION5( CHAIN A AND RESID 205:230 )A205 - 230
6X-RAY DIFFRACTION6( CHAIN A AND RESID 231:248 )A231 - 248
7X-RAY DIFFRACTION7( CHAIN A AND RESID 249:281 )A249 - 281
8X-RAY DIFFRACTION8( CHAIN A AND RESID 282:296 )A282 - 296
9X-RAY DIFFRACTION9( CHAIN B AND RESID 71:92 )B71 - 92
10X-RAY DIFFRACTION10( CHAIN B AND RESID 93:112 )B93 - 112
11X-RAY DIFFRACTION11( CHAIN B AND RESID 113:136 )B113 - 136
12X-RAY DIFFRACTION12( CHAIN B AND RESID 137:230 )B137 - 230
13X-RAY DIFFRACTION13( CHAIN B AND RESID 231:248 )B231 - 248
14X-RAY DIFFRACTION14( CHAIN B AND RESID 249:260 )B249 - 260
15X-RAY DIFFRACTION15( CHAIN B AND RESID 261:280 )B261 - 280
16X-RAY DIFFRACTION16( CHAIN B AND RESID 281:296 )B281 - 296
17X-RAY DIFFRACTION17( CHAIN C AND RESID 73:92 )C73 - 92
18X-RAY DIFFRACTION18( CHAIN C AND RESID 93:112 )C93 - 112
19X-RAY DIFFRACTION19( CHAIN C AND RESID 113:135 )C113 - 135
20X-RAY DIFFRACTION20( CHAIN C AND RESID 136:161 )C136 - 161
21X-RAY DIFFRACTION21( CHAIN C AND RESID 162:212 )C162 - 212
22X-RAY DIFFRACTION22( CHAIN C AND RESID 213:230 )C213 - 230
23X-RAY DIFFRACTION23( CHAIN C AND RESID 231:248 )C231 - 248
24X-RAY DIFFRACTION24( CHAIN C AND RESID 249:272 )C249 - 272
25X-RAY DIFFRACTION25( CHAIN C AND RESID 273:281 )C273 - 281
26X-RAY DIFFRACTION26( CHAIN C AND RESID 282:296 )C282 - 296
27X-RAY DIFFRACTION27( CHAIN D AND RESID 73:92 )D73 - 92
28X-RAY DIFFRACTION28( CHAIN D AND RESID 93:136 )D93 - 136
29X-RAY DIFFRACTION29( CHAIN D AND RESID 137:210 )D137 - 210
30X-RAY DIFFRACTION30( CHAIN D AND RESID 211:234 )D211 - 234
31X-RAY DIFFRACTION31( CHAIN D AND RESID 235:248 )D235 - 248
32X-RAY DIFFRACTION32( CHAIN D AND RESID 249:272 )D249 - 272
33X-RAY DIFFRACTION33( CHAIN D AND RESID 273:296 )D273 - 296

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