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- PDB-1j59: CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3... -

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Basic information

Entry
Database: PDB / ID: 1j59
TitleCATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Components
  • 5'-D(*AP*TP*AP*TP*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G )-3'
  • 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3'
  • CATABOLITE GENE ACTIVATOR PROTEIN (CAP)
KeywordsGENE REGULATION/DNA / PROTEIN-DNA COMPLEX / GENE-REGULATORY / GENE REGULATION-DNA COMPLEX
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 / identical protein binding / cytosol
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / 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
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / DNA-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsParkinson, G. / Wilson, C. / Gunasekera, A. / Ebright, Y.W. / Ebright, R.H. / Berman, H.M.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface.
Authors: Parkinson, G. / Wilson, C. / Gunasekera, A. / Ebright, Y.W. / Ebright, R.E. / Berman, H.M.
History
SupersessionMar 1, 2002ID: 1BER
DepositionMar 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3'
D: 5'-D(*AP*TP*AP*TP*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G )-3'
E: 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3'
F: 5'-D(*AP*TP*AP*TP*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G )-3'
A: CATABOLITE GENE ACTIVATOR PROTEIN (CAP)
B: CATABOLITE GENE ACTIVATOR PROTEIN (CAP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7538
Polymers66,0956
Non-polymers6582
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.990, 152.800, 76.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3'


Mass: 4353.854 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*TP*AP*TP*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G )-3'


Mass: 5152.358 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein CATABOLITE GENE ACTIVATOR PROTEIN (CAP)


Mass: 23541.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACJ8
#4: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 58.71 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: vapor diffusion, sitting drop / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMMES-NaOH1reservoirpH6.5
2200 mM1reservoirNaCl
3100 mM1reservoirMgCl2
4100 mM1reservoirCaCl2
50.02 %(w/v)1reservoirNaN3
62 mMdithiothreitol1reservoir
72 mMspermine1reservoir
82 mMcAMP1reservoir
90.3 %(w/v)n-octyl-beta-D-glucopyranoside1reservoir
106.5 %(w/v)PEG33501reservoir
110.1-0.2 mMCAP1drop
12DNA1drop1.2-1.5fold molar excess

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23876 / % possible obs: 85.4 % / Rmerge(I) obs: 0.1147 / Net I/σ(I): 2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % possible obs: 84.9 % / Num. measured all: 165000

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.279 --
Rwork0.199 --
obs0.199 23644 86 %
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 1262 42 286 4718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 27527
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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