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- PDB-2m1b: Solution structure of the CHXR DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 2m1b
TitleSolution structure of the CHXR DNA-binding domain
ComponentsTranscriptional regulatory protein, C terminal family protein
KeywordsTRANSCRIPTION REGULATOR / OMPR
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHickey, J.M. / Anbanandam, A.M. / Hefty, S.P.
CitationJournal: Plos One / Year: 2014
Title: Atypical response regulator ChxR from Chlamydia trachomatis is structurally poised for DNA binding.
Authors: Barta, M.L. / Hickey, J.M. / Anbanandam, A. / Dyer, K. / Hammel, M. / Hefty, P.S.
History
DepositionNov 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein, C terminal family protein


Theoretical massNumber of molelcules
Total (without water)13,7881
Polymers13,7881
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulatory protein, C terminal family protein


Mass: 13787.905 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: L2/434/BU / Gene: CTL0894, CTL2C_660 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F9YCU1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CO)CA
1413D HNCO
1513D HBHA(CO)N 3D HN(CA)CB
1613D CBCA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-1 NOESY
11212D 1H-13C HSQC
NMR detailsText: Solution NMR structure was determined using noe distance and TALOS+ based dihedral angles

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Sample preparation

DetailsContents: 1.5 mM [U-100% 13C; U-100% 15N] TRANSCRIPTIONAL REGULATORY PROTEIN, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: TRANSCRIPTIONAL REGULATORY PROTEIN-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER, ADAMS, CLORE, GROS, NILGESrefinement
SparkyGoddardstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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