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- PDB-5aiw: NMR solution structure of the putative transfer protein TraH from... -

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Basic information

Entry
Database: PDB / ID: 5aiw
TitleNMR solution structure of the putative transfer protein TraH from Gram-positive conjugative plasmid pIP501
ComponentsTRAH
KeywordsCELL ADHESION / BACTERIAL / BACTERIAL CONJUGATION
Function / homologyTRAH / :
Function and homology information
Biological speciesENTEROCOCCUS FAECALIS ENGEN0234 (bacteria)
MethodSOLUTION NMR / CYANA, CNS
AuthorsMeyer, N.H. / Fercher, C. / Zangger, K. / Keller, W.
CitationJournal: Sci.Rep. / Year: 2016
Title: Virb8-Like Protein Trah is Crucial for DNA Transfer in Enterococcus Faecalis.
Authors: Fercher, C. / Probst, I. / Kohler, V. / Goessweiner-Mohr, N. / Arends, K. / Grohmann, E. / Zangger, K. / Meyer, N.H. / Keller, W.
History
DepositionFeb 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAH


Theoretical massNumber of molelcules
Total (without water)14,9141
Polymers14,9141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein TRAH


Mass: 14914.358 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 57-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS ENGEN0234 (bacteria)
Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: R4CA00, UniProt: A0A140UHJ9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED TRAH

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Sample preparation

DetailsContents: 10% D2O, 90% WATER
Sample conditionsIonic strength: 200 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
RECOORD CNSCNSA.J. NEDERVEEN, J.F. DORELEIJERS, W.F. VRANKEN, Z. MILLER, C.A.E.M. SPRONK, S.B. NABUURS, P. GUENTERT, M. LIVNY, J.L. MARKLEY, M. NILGES, E.L. ULRICH, R. KAPTEINrefinement
CYANAstructure solution
CNSstructure solution
RefinementMethod: CYANA, CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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