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- PDB-2jny: Solution NMR structure of protein Uncharacterized BCR, Northeast ... -

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Basic information

Entry
Database: PDB / ID: 2jny
TitleSolution NMR structure of protein Uncharacterized BCR, Northeast Structural Genomics Consortium target CgR1
ComponentsUncharacterized BCR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / cgr1 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyTrm112-like / Trm112p-like protein / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Mainly Beta / UPF0434 protein Cgl1405
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, Y. / Liu, G. / Zhang, Q. / Chen, C. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M. ...Wu, Y. / Liu, G. / Zhang, Q. / Chen, C. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G. / Acton, T. / Rost, B. / Montelione, G. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of protein Uncharacterized BCR, Northeast Structural Genomics Consortium target CgR1
Authors: Wu, Y. / Liu, G. / Zhang, Q. / Chen, C. / Nwosu, C. / Cunningham, K. / Ma, L. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G. / Rost, B. / Montelione, G. / Szyperski, T.
History
DepositionFeb 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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
Revision 1.6May 8, 2024Group: Database references / Category: 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: Uncharacterized BCR


Theoretical massNumber of molelcules
Total (without water)7,8131
Polymers7,8131
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 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Uncharacterized BCR / Hypothetical protein


Mass: 7812.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NQM9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111SIMULTANEOUS HETERONUCLEAR RESOLVED [1H,1H]-NOESY
121GFT (4,3)D HNNCABCA
131GFT (4,3)D CABCA(CO)NHN
141GFT (4,3)D HABCAB(CO)NHN
151GFT (4,3)D (H)CCH

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] Uncharacterized BCR - label 1, 1.0 mM [U-5% 13C; U-100% 15N] Uncharacterized BCR - label 2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMUncharacterized BCR - label 1[U-100% 13C; U-100% 15N]1
1.0 mMUncharacterized BCR - label 2[U-5% 13C; U-100% 15N]1
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 25 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
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.peak picking
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoAssignZimmerman, Moseley, Kulikowski, Montelionechemical shift assignment
AutoStructureHuang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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