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- PDB-2l5q: Solution NMR Structure of BVU_3817 from Bacteroides vulgatus, Nor... -

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Basic information

Entry
Database: PDB / ID: 2l5q
TitleSolution NMR Structure of BVU_3817 from Bacteroides vulgatus, Northeast Structural Genomics Consortium Target BvR159
ComponentsUncharacterized protein
KeywordsStructural genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #1650 / SH3 type barrels. - #730 / Domain of unknown function DUF5606 / Domain of unknown function (DUF5606) / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DUF5606 domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodSOLUTION NMR
Model detailslowest energy, model 1
AuthorsMills, J.L. / Eletsky, A. / Lee, H. / Wang, H. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. ...Mills, J.L. / Eletsky, A. / Lee, H. / Wang, H. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target BvR159
Authors: Mills, J.L. / Eletsky, A. / Lee, H. / Wang, H. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionNov 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Mar 7, 2012Group: Database references / Structure summary
Revision 1.4Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Jun 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 1.6May 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,8951
Polymers15,8951
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 15895.229 Da / Num. of mol.: 1 / Fragment: sequence database residues 61-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_3817 / Production host: Escherichia coli (E. coli) / References: UniProt: A6L6W4

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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
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-COSY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HBHA(CO)NH
1913D HN(CA)CO
11022D 1H-13C HSQC
11132D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.78 mM [U-98% 13C; U-98% 15N] BvR159, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 5 % D2O, 95 % H2O, 95% H2O/5% D2O95% H2O/5% D2O
20.66 mM [5% U-98% 13C; U-98% 15N] BvR159, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 5 % D2O, 95 % H2O, 95% H2O/5% D2O95% H2O/5% D2O
30.61 mM [5% U-98% 13C; U-98% 15N] BvR159, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 5 % D2O, 95 % H2O, 7 % PAGE, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.78 mMBvR159-1[U-98% 13C; U-98% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
0.02 %sodium azide-41
10 mMTRIS-51
5 %D2O-61
95 %H2O-71
0.66 mMBvR159-8[5% U-98% 13C; U-98% 15N]2
100 mMsodium chloride-92
5 mMDTT-102
0.02 %sodium azide-112
10 mMTRIS-122
5 %D2O-132
95 %H2O-142
0.61 mMBvR159-15[5% U-98% 13C; U-98% 15N]3
100 mMsodium chloride-163
5 mMDTT-173
0.02 %sodium azide-183
10 mMTRIS-193
5 %D2O-203
95 %H2O-213
7 %PAGE-223
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller et al.data analysis
CARAKeller et al.peak picking
CARAKeller et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PROSAGuntertprocessing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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