[English] 日本語
Yorodumi
- PDB-6k93: Crystal structure of the type III effector XopAI from Xanthomonas... -

+
Open data


ID or keywords:

Loading...

-
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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more