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- PDB-7mu9: Solution NMR structure of the XVIPCD region from the T4SS effecto... -

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Basic information

Entry
Database: PDB / ID: 7mu9
TitleSolution NMR structure of the XVIPCD region from the T4SS effector X-Tfe(XAC2609) from Xanthomonas citri
ComponentsVirD4 interacting protein conserved domain
KeywordsTRANSPORT PROTEIN / bacterial toxin / bacterial competition / type IV secretion system / VirD4 binding module
Function / homologyPGBD superfamily / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / carboxypeptidase activity / Lysozyme-like domain superfamily / Carboxypeptidase
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsOka, G.U. / Salinas, R.K. / Farah, C.S.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2017/17303-7 Brazil
Sao Paulo Research Foundation (FAPESP)2018/09277-9 Brazil
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural basis for effector recognition by an antibacterial type IV secretion system.
Authors: Oka, G.U. / Souza, D.P. / Cenens, W. / Matsuyama, B.Y. / Cardoso, M.V.C. / Oliveira, L.C. / da Silva Lima, F. / Cuccovia, I.M. / Guzzo, C.R. / Salinas, R.K. / Farah, C.S.
History
DepositionMay 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: VirD4 interacting protein conserved domain


Theoretical massNumber of molelcules
Total (without water)11,4811
Polymers11,4811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein VirD4 interacting protein conserved domain / carboxypeptidase / VIPCD


Mass: 11480.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC2609 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): RP / References: UniProt: Q8PJC6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
191anisotropic13D HN(CA)CB
1101anisotropic13D CBCA(CO)NH
1111anisotropic13D HNCA
1121anisotropic13D HN(CO)CA
1131anisotropic13D HNCO
1141anisotropic1HN(CA)CO
1151isotropic13D-(H)CCH
1161anisotropic13D-H(C)CH
1171anisotropic13D (H)CCH-TOCSY
1181anisotropic13D (H)CCH-TOCSY
1191anisotropic13D 15N NOESY-HSQC
1201anisotropic13D 13C NOESY-HSQC
1211anisotropic12D 1H-1H NOESY
1221anisotropic12D AROMATIC 13C NOESY-HSQC
1231anisotropic13D (D2O) H(C)CH-TOCSY
1241anisotropic13D (D2O) (H)CCH-TOCSY
1251anisotropic13D (D2O) 13C NOESY-HSQC
1261anisotropic13D (D2) 15N NOESY-HSQC
1271anisotropic12D 1H-13C HSQC
1281anisotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-100% 13C; U-100% 15N] XAC2609(311-411), 20 mM TRIS, 100 mM sodium chloride, 0.1 % v/v glycerol, 0.05 % w/v sodium azide, 93% H2O/7% D2O
Label: 15N/13C / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMXAC2609(311-411)[U-100% 13C; U-100% 15N]1
20 mMTRISnatural abundance1
100 mMsodium chloridenatural abundance1
0.1 % v/vglycerolnatural abundance1
0.05 % w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 100 mM NaCl mM / Label: condition_1 / pH: 8 / PH err: 0.1 / Pressure: 1016 mbar / Pressure err: 10 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.3CCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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