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- PDB-1ruo: CATABOLITE GENE ACTIVATOR PROTEIN (CAP) MUTANT/DNA COMPLEX + ADEN... -

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Basic information

Entry
Database: PDB / ID: 1ruo
TitleCATABOLITE GENE ACTIVATOR PROTEIN (CAP) MUTANT/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Components
  • DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*G )-3')
  • DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
  • PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP))
KeywordsTRANSCRIPTION/DNA / GENE-REGULATORY PROTEIN-DNA COMPLEX / COMPLEX (GENE-REGULATORY PROTEIN-DNA) / TRANSCRIPTION REGULATION / DNA-BINDING / CAMP-BINDING / ACTIVATOR / TRANSCRIPTION-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: 2.7 Å
AuthorsParkinson, G.N. / Ebright, R.H. / Berman, H.M.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Aromatic hydrogen bond in sequence-specific protein DNA recognition.
Authors: Parkinson, G. / Gunasekera, A. / Vojtechovsky, J. / Zhang, X. / Kunkel, T.A. / Berman, H. / Ebright, R.H.
History
DepositionMay 26, 1996Processing site: NDB
Revision 1.0Jan 10, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*G )-3')
E: DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
F: DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*G )-3')
A: PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP))
B: PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7878
Polymers66,1296
Non-polymers6582
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.290, 153.100, 76.200
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 DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')


Mass: 4352.867 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*G )-3')


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


Mass: 23559.303 Da / Num. of mol.: 2 / Mutation: CHAIN A, B, E181F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Keywords: MUTANT CHAIN A, B, E181F / 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.: 35 / 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: 58.95 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.UnitCommon nameSol-IDChemical formulaDetails
10.1-0.2 mMCAPdrop
350 mMMes-NaOHreservoir
4200 mMreservoirNaCl
5100 mMreservoirMgCl2
6100 mMreservoirCaCl2
70.02 %(w/v)reservoirNaN3
82 mMdithiothreitolreservoir
92 mMsperminereservoir
2%(v/v)DNA molecule 31-2Edrop1.2- to 1.5-molar excess
102 mMcAMPreservoir
110.3 %(w/v)n-octyl-beta-D-glucopyranosidereservoir
126.5 %(w/v)PRG3350reservoir
1350 %well bufferdrop

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Data collection

DiffractionMean temperature: 258 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 18147 / % possible obs: 83.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1062
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 40 Å / % possible obs: 83.7 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Num. measured all: 52283 / Rmerge(I) obs: 0.105

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Processing

Software
NameVersionClassification
PURDUESOFTWAREdata collection
X-PLORrefinement
PURDUEDATA PROCESSING PACKAGEdata reduction
RefinementResolution: 2.7→10 Å / σ(F): 4
RfactorNum. reflection% reflection
Rwork0.213 --
obs-17328 78.9 %
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 1262 44 35 4512
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRODNA-RNA-MULTI-ENDO.PARAM
X-RAY DIFFRACTION2TOPHCSDX.PRODNA-RNA-MULTI-ENDO.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 4 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.42
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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