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- PDB-2l02: Solution NMR Structure of protein BT2368 from Bacteroides thetaio... -

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Basic information

Entry
Database: PDB / ID: 2l02
TitleSolution NMR Structure of protein BT2368 from Bacteroides thetaiotaomicron, Northeast Structural Genomics Consortium Target BtR375
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homologyWinged helix-turn-helix domain (DUF2582) / Winged helix-turn-helix domain (DUF2582) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / cytoplasm / Winged helix-turn-helix domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Lee, H. / Wang, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. ...Eletsky, A. / Lee, H. / Wang, D. / 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: Solution NMR Structure of protein BT2368 from Bacteroides thetaiotaomicron
Authors: Eletsky, A. / Lee, H. / Wang, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / 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 1.3Jun 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 1.4May 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
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,4412
Polymers18,4412
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 9220.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2368 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8A574

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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 CT-HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-13C CT-HSQC aromatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HN(CA)CO
1913D HBHA(CO)NH
11013D (H)CCH-COSY aliphatic
11113D (H)CCH-COSY aromatic
11213D (H)CCH-TOCSY aliphatic
11322D 1H-13C CT-HSQC methyl
11422D J-modulation 1H-15N HSQC
11532D J-modulation 1H-15N HSQC
11642D J-modulation 1H-15N HSQC
11712D 1H-15N LR-HSQC for Histidine

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] BtR375, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-5% 13C; U-100% 15N] BtR375, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-5% 13C; U-100% 15N] BtR375, 18 mM ammonium acetate, 91 mM sodium chloride, 4.6 mM calcium chloride, 0.018 % sodium azide, 4 % C12E5 polyethylene glycol, 4 % hexanol, 80% H2O/20% D2O80% H2O/20% D2O
41.2 mM [U-5% 13C; U-100% 15N] BtR375, 18 mM ammonium acetate, 91 mM sodium chloride, 4.6 mM calcium chloride, 0.018 % sodium azide, 80% H2O/20% D2O80% H2O/20% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMBtR375-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
1.1 mMBtR375-6[U-5% 13C; U-100% 15N]2
20 mMammonium acetate-72
100 mMsodium chloride-82
5 mMcalcium chloride-92
0.02 %sodium azide-102
0.9 mMBtR375-11[U-5% 13C; U-100% 15N]3
18 mMammonium acetate-123
91 mMsodium chloride-133
4.6 mMcalcium chloride-143
0.018 %sodium azide-153
4 %C12E5 polyethylene glycol-163
4 %hexanol-173
1.2 mMBtR375-18[U-5% 13C; U-100% 15N]4
18 mMammonium acetate-194
91 mMsodium chloride-204
4.6 mMcalcium chloride-214
0.018 %sodium azide-224
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3.13Bartels et al.data analysis
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
VnmrJ2.1BVariancollection
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
PROSA6.4Guntertprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA 3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and backbone H-N residual dipolar couplings ...Details: Structure determination was performed iteratively with CYANA 3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and backbone H-N residual dipolar couplings from two alignment media. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field and upper limit constraints relaxed by 5%
NMR constraintsNOE constraints total: 2264 / NOE intraresidue total count: 477 / NOE long range total count: 526 / NOE medium range total count: 679 / NOE sequential total count: 582 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 122 / Protein psi angle constraints total count: 122
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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