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- PDB-2jn6: Solution NMR structure of Protein Cgl2762 from Corynebacterium Gl... -

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Basic information

Entry
Database: PDB / ID: 2jn6
TitleSolution NMR structure of Protein Cgl2762 from Corynebacterium Glutamicum: Northeast Structural Genomics Consortium Target CgR3
ComponentsProtein Cgl2762
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT NMR / PSI-2 / Protein structure / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding
Similarity search - Function
Transposase IS3/IS911family / Transposase / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSingarapu, K.K. / Sukumaran, D.K. / Parish, D. / Chen, C.X. / Cunningham, K. / Xiao, R. / Swapna, G.V.T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2008
Title: NMR structure of protein Cgl2762 from Corynebacterium glutamicum implicated in DNA transposition reveals a helix-turn-helix motif attached to a flexibly disordered leucine zipper.
Authors: Singarapu, K.K. / Xiao, R. / Sukumaran, D.K. / Acton, T. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _struct_ref_seq_dif.details
Revision 1.4Jun 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 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Cgl2762


Theoretical massNumber of molelcules
Total (without water)11,0451
Polymers11,0451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein Cgl2762 / Transposase


Mass: 11045.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: XL10 / Gene: tnp8a ISCg8a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+magic / References: UniProt: Q8NM20

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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
1314,3D GFT HNNCABCA
1414,3D GFT CABCACONNH
1514,3D GFT HABCABCONNH
1614,3D (H)CCH COSY
1713D (H)CCH-COSY
1813D 13C,15N simultaneous NOESY
1913D HNCO

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Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N] hypothetical protein Cgl2762, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.2 mM / Component: hypothetical protein Cgl2762 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
DYANA1.5Guntert, Braun and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
AutoStructure2Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionedata analysis
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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