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- PDB-2lio: Solution NMR Structure of BfR322 from Bacteroides fragilis, North... -

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Basic information

Entry
Database: PDB / ID: 2lio
TitleSolution NMR Structure of BfR322 from Bacteroides fragilis, Northeast Structural Genomics Consortium Target BfR322
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homologySTART-like domain / START-like superfamily domain / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / START-like domain-containing protein
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailslowest energy, model 1
AuthorsMills, J.L. / Lee, H. / Lee, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Mills, J.L. / Lee, H. / Lee, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / 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 BfR322
Authors: Mills, J.L. / Lee, H. / Lee, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionAug 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,1221
Polymers16,1221
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: 16121.950 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BF0592 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64YT5

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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 HBHA(CO)NH
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
181(H)CCH-TOCSY
191(H)CCH-COSY
11032D 1H-15N HSQC
11122D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.65 mM [U-100% 13C; U-100% 15N] BfR322, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
20.86 mM [U-5% 13C; U-100% 15N] BfR322, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
30.86 mM [U-10% 13C; U-100% 15N] BfR322, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 12.5 mg/ml phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMBfR322-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
0.02 %sodium azide-41
10 mMTRIS-51
0.86 mMBfR322-6[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-72
5 mMDTT-82
0.02 %sodium azide-92
10 mMTRIS-102
0.86 mMBfR322-11[U-10% 13C; U-100% 15N]3
100 mMsodium chloride-123
5 mMDTT-133
0.02 %sodium azide-143
10 mMTRIS-153
12.5 mg/mLphage-163
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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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
PROSAGuntertprocessing
CARAKeller et al.data analysis
CARAKeller et al.peak picking
CARAKeller et al.chemical shift assignment
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1
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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