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- PDB-2k9q: Solution NMR structure of HTH_XRE family transcriptional regulato... -

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Basic information

Entry
Database: PDB / ID: 2k9q
TitleSolution NMR structure of HTH_XRE family transcriptional regulator BT_p548217 from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR244.
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / all helix / helix-turn-helix / Plasmid / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


cAMP-dependent Protein Kinase, Chain A - #30 / cAMP-dependent Protein Kinase, Chain A / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Helix non-globular / Special / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsHTH_XRE superfamily protein all helix HTH_3 helix-turn-helix
AuthorsRamelot, T.A. / Cort, J.R. / Zhao, L. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Ramelot, T.A. / Cort, J.R. / Zhao, L. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of HTH_XRE family transcriptional regulator BT_p548217 from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium Target BtR244.
Authors: Ramelot, T.A. / Cort, J.R. / Zhao, L. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionOct 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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 8, 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)17,7772
Polymers17,7772
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 / 150structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein uncharacterized protein


Mass: 8888.267 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Species: thetaiotaomicron / Gene: BT_p548217, p5482_17 / Plasmid: pET21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q8ABY1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: HTH_XRE superfamily protein all helix HTH_3 helix-turn-helix
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1342D 1H-13C HSQC
1432D 1H-13C HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1724D 1H-13C NOESY
1813D HNCO
1923D 1H-13C NOESY
11013D HNCA
11113D HN(CO)CA
11213D CBCA(CO)NH
11313D HN(CA)CB
11413D C(CO)NH
11513D HBHA(CO)NH
11613D (H)CCH-TOCSY
11713D (H)CCH-COSY
11822D 1H-15N HSQC
11922D 1H-13C HSQC
12033D 1H-13C ED-FILT NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 0.9 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
220 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, .9 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
320 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, .5 mM [U-100% 13C; U-100% 15N] protein, .5 mM protein, 95% H2O/5% D2O95% H2O/5% D2O
420 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 1 mM [U-5% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMammonium acetate1
100 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
0.9 mMprotein[U-100% 13C; U-100% 15N]1
20 mMammonium acetate2
100 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
.9 mMprotein[U-100% 13C; U-100% 15N]2
20 mMammonium acetate3
100 mMsodium chloride3
5 mMcalcium chloride3
10 mMDTT3
0.02 %sodium azide3
.5 mMprotein-1[U-100% 13C; U-100% 15N]3
.5 mMprotein-23
20 mMammonium acetate4
100 mMsodium chloride4
5 mMcalcium chloride4
10 mMDTT4
0.02 %sodium azide4
1 mMprotein[U-5% 13C; U-100% 15N]4
Sample conditionsIonic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Bruker AvanceIIIBrukerAVANCE III8503
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5(PDBStat) R. Tejero, G.T. Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NIH-Xplor-2.20 refinement with hydrogen bond PMF, radius of gyration, etc.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 150 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4.1 ° / Maximum upper distance constraint violation: 0.28 Å

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