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- PDB-2wc2: Nmr structure of catabolite activator protein in the unliganded state -

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Basic information

Entry
Database: PDB / ID: 2wc2
TitleNmr structure of catabolite activator protein in the unliganded state
ComponentsCATABOLITE GENE ACTIVATOR
KeywordsTRANSCRIPTION REGULATOR / TRANSCTIPTION FACTOR / TRANSCRIPTION REGULATION / CYCLIC NUCLEOTIDE-BINDING PROTEIN / CAMP-BINDING / TRANSCRIPTION / ALLOSTERIC PROTEIN / CATABOLITE ACTIVATOR PROTEIN / NUCLEOTIDE-BINDING / DNA-BINDING PROTEIN / CAMP / ACTIVATOR / ACETYLATION / DNA-BINDING
Function / homology
Function and homology information


carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription ...carbon catabolite repression of transcription / DNA binding, bending / minor groove of adenine-thymine-rich DNA binding / cAMP binding / protein-DNA complex / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol
Similarity search - Function
Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain ...Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA-binding transcriptional dual regulator CRP / cAMP-activated global transcriptional regulator CRP
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsPopovych, N. / Tzeng, S.R. / Kalodimos, C.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural Basis for Camp-Mediated Allosteric Control of the Catabolite Activator Protein.
Authors: Popovych, N. / Tzeng, S.R. / Tonelli, M. / Ebright, R.H. / Kalodimos, C.G.
History
DepositionMar 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 15, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_validate_close_contact.auth_atom_id_2
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATABOLITE GENE ACTIVATOR
B: CATABOLITE GENE ACTIVATOR


Theoretical massNumber of molelcules
Total (without water)47,0822
Polymers47,0822
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 / 200LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein CATABOLITE GENE ACTIVATOR / CATABOLITE ACTIVATOR PROTEIN / CAMP RECEPTOR PROTEIN / CAMP REGULATORY PROTEIN


Mass: 23541.242 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACK0, UniProt: P0ACJ8*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CO)CA
131HNCO
141HN(CA)CO
151HN(CA)CB
1613D-15N- NOESY
1713D-13C-NOESY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90%WATER/10%D2O, 100%D2O
Sample conditionsIonic strength: 500 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 305.0 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
HADDOCK-CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
ARIAstructure solution
HADDOCKstructure solution
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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