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- PDB-2l8b: TraI (381-569) -

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Basic information

Entry
Database: PDB / ID: 2l8b
TitleTraI (381-569)
ComponentsProtein traI
KeywordsHYDROLASE / RecD
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / metabolic process / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase ...DNA helicase, TraI type / Conjugative transfer relaxase protein TraI / TraI, 2B/2B-like domain / TraI, N-terminal subdomain / DNA helicase TraI, C-terminal / single-stranded DNA binding TraI N-terminal subdomain / DNA relaxase TraI 2B/2B-like domain / Conjugative relaxase, N-terminal / TrwC relaxase / TrwC relaxase / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Multifunctional conjugation protein TraI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsWright, N.T. / Raththagala, M.U. / Edwards, S. / Krueger, S. / Schildbach, J.F.
CitationJournal: Proteins / Year: 2012
Title: Solution structure and small angle scattering analysis of TraI (381-569).
Authors: Wright, N.T. / Raththagala, M. / Hemmis, C.W. / Edwards, S. / Curtis, J.E. / Krueger, S. / Schildbach, J.F.
History
DepositionJan 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Feb 8, 2023Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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
Revision 1.4May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein traI


Theoretical massNumber of molelcules
Total (without water)20,4941
Polymers20,4941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein traI / DNA helicase I


Mass: 20494.223 Da / Num. of mol.: 1 / Fragment: sequence database residues 381-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECOK12F104, traI / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P14565, DNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of F-plasmid TraI, residue 381-569
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 20 mM TRIS, 20 mM sodium chloride, 1 mM EDTA, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMTRIS-11
20 mMsodium chloride-21
1 mMEDTA-31
10 %D2O-41
Sample conditionsIonic strength: 0.04 / pH: 7.2 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2204 / NOE intraresidue total count: 519 / NOE long range total count: 481 / NOE medium range total count: 468 / NOE sequential total count: 596 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.4 Å
NMR ensemble rmsDistance rms dev: 0.037 Å / Distance rms dev error: 0.002 Å

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