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- PDB-2l8n: NMR structure of the cytidine repressor DNA binding domain in pre... -

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Basic information

Entry
Database: PDB / ID: 2l8n
TitleNMR structure of the cytidine repressor DNA binding domain in presence of operator half-site DNA
ComponentsTranscriptional repressor CytR
KeywordsTRANSCRIPTION REGULATOR / BACTERIAL GENE REPRESSOR / HELIX TURN HELIX BINDING DOMAIN / LACR FAMILY / REPRESSOR / TRANSCRIPTION / TRANSCRIPTION REGULATION / DNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional repressor CytR / Transcriptional repressor CytR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMoody, C.L. / Tretyachenko-Ladokhina, V. / Senear, D.F. / Cocco, M.J.
CitationJournal: Biochemistry / Year: 2011
Title: Multiple Conformations of the Cytidine Repressor DNA-Binding Domain Coalesce to One upon Recognition of a Specific DNA Surface.
Authors: Moody, C.L. / Tretyachenko-Ladokhina, V. / Laue, T.M. / Senear, D.F. / Cocco, M.J.
History
DepositionJan 20, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
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: Transcriptional repressor CytR


Theoretical massNumber of molelcules
Total (without water)7,4031
Polymers7,4031
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)11 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional repressor CytR


Mass: 7402.625 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN RESIDUES 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 536 / UPEC / Gene: B3934, CYTR, ECP_4143, JW3905 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: Q0TAD0, UniProt: A0A454AAE4*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1413D 1H-15N NOESY
1513D 1H-15N TOCSY
1623D 1H-13C NOESY
172(H)CCH-TOCSY
2832D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.411 mM [U-15N] HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR, 1.14 mM ATTTATGCAACGCA DNA, 50 mM sodium phosphate, 30 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR, 1.2 mM ATTTATGCAACGCA DNA, 50 mM sodium phosphate, 30 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-15N] HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR, 0.6 mM ATTTATGCAACGCA DNA, 50 mM sodium phosphate, 30 mM sodium chloride, 1 mM EDTA, 4 % C12E5 PEG/HEXANOL, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.411 mMHTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR-1[U-15N]1
1.14 mMATTTATGCAACGCA DNA-21
50 mMsodium phosphate-31
30 mMsodium chloride-41
1 mMEDTA-51
1 mMHTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR-6[U-13C; U-15N]2
1.2 mMATTTATGCAACGCA DNA-72
50 mMsodium phosphate-82
30 mMsodium chloride-92
1 mMEDTA-102
0.4 mMHTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR-11[U-15N]3
0.6 mMATTTATGCAACGCA DNA-123
50 mMsodium phosphate-133
30 mMsodium chloride-143
1 mMEDTA-153
4 %C12E5 PEG/HEXANOL-163
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.0576AMBIENT 308 K
20.0576AMBIENT 298 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, TJrefinement
VNMRVarianstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
ANALYSIS_-_CCPNCCPNstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 557 / NOE intraresidue total count: 234 / NOE long range total count: 41 / NOE medium range total count: 148 / NOE sequential total count: 134 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 37
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 11

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