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- PDB-2n01: NMR structure of VirB9 C-terminal domain in complex with VirB7 N-... -

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Basic information

Entry
Database: PDB / ID: 2n01
TitleNMR structure of VirB9 C-terminal domain in complex with VirB7 N-terminal domain from Xanthomonas citri's T4SS
Components
  • VirB7 protein
  • VirB9 protein
KeywordsPROTEIN TRANSPORT/PROTEIN TRANSPORT / T4SS / lipoprotein / protein-peptide complex / VirB9 / VirB7 / PROTEIN TRANSPORT-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


Immunoglobulin-like - #2500 / Toxin co-regulated pilus biosynthesis protein Q, C-terminal / Toxin co-regulated pilus biosynthesis protein Q / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Toxin co-regulated pilus biosynthesis protein Q C-terminal domain-containing protein / VirB9 protein
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodSOLUTION NMR / simulated annealing, water refinement in cartesian space
AuthorsOliveira, L.C. / Souza, D.P. / Salinas, R.K. / Wienk, H. / Boelens, R. / Farah, S.C.
CitationJournal: Structure / Year: 2016
Title: VirB7 and VirB9 Interactions Are Required for the Assembly and Antibacterial Activity of a Type IV Secretion System.
Authors: Oliveira, L.C. / Souza, D.P. / Oka, G.U. / Lima, F.D. / Oliveira, R.J. / Favaro, D.C. / Wienk, H. / Boelens, R. / Farah, C.S. / Salinas, R.K.
History
DepositionMar 3, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VirB7 protein
B: VirB9 protein


Theoretical massNumber of molelcules
Total (without water)15,1372
Polymers15,1372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area8780 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide VirB7 protein


Mass: 2665.913 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 24-46) / Source method: obtained synthetically
Source: (synth.) Xanthomonas axonopodis pv. citri (bacteria)
References: UniProt: Q8PJB3
#2: Protein VirB9 protein


Mass: 12471.122 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 154-255)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: virB9, XAC2620, XAC2622 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PJB5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D C(CO)NH
1813D HNCO
1913D HNCA
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11413D CCH TOCSY
11513D HN(CA)CB
11613D 15N, 13C CNH-NOESY
11712D 13C15N filtered NOE
11812D 13C,15N filtered TOCSY
11913D (HB)CB(CGCD)HD
12013D 15N-edited NOESY
12113D 13C-edited NOESY
12213D HN(CO)CA
12313D HN(CA)CO
12413D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 0.500 mM [U-99% 13C; U-99% 15N] Xac_VirB9CT, 1 mM Xac_VirB7NT, 20 mM [U-100% 2H] sodium acetate, 50 mM sodium chloride, 1 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMXac_VirB9CT-1[U-99% 13C; U-99% 15N]1
1 mMXac_VirB7NT-21
20 mMsodium acetate-3[U-100% 2H]1
50 mMsodium chloride-41
1 %sodium azide-51
Sample conditionsIonic strength: 0.07 / pH: 5.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIIBrukerAVANCE III8001
Bruker Avance IIIBrukerAVANCE III9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.4.1CCPNdata analysis
RefinementMethod: simulated annealing, water refinement in cartesian space
Software ordinal: 1
Details: RECALCULATION USING RECOORD SCRIPTS, WATER REFINEMENT USING RECOORD SCRIPTS
NMR constraintsNOE constraints total: 2216 / NOE intraresidue total count: 535 / NOE long range total count: 767 / NOE medium range total count: 239 / NOE sequential total count: 675 / Hydrogen bond constraints total count: 78 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 70 / Protein psi angle constraints total count: 70
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.285 Å
NMR ensemble rmsDistance rms dev: 0.0143283 Å

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