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- PDB-2cgp: CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CY... -

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Basic information

Entry
Database: PDB / ID: 2cgp
TitleCATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Components
  • DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')
  • DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3')
  • PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN)
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPassner, J.M. / Steitz, T.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer.
Authors: Passner, J.M. / Steitz, T.A.
#1: Journal: Science / Year: 1991
Title: Crystal Structure of a CAP-DNA Complex: The DNA is Bent by 90 Degrees
Authors: Schultz, S.C. / Shields, G.C. / Steitz, T.A.
History
DepositionJan 31, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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
B: DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')
A: PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2705
Polymers31,6123
Non-polymers6582
Water2,684149
1
B: DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')
A: PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)64,54010
Polymers63,2236
Non-polymers1,3174
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)79.190, 79.190, 140.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3')


Mass: 3332.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')


Mass: 4607.033 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN)


Mass: 23672.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 60 %
Crystal growpH: 6
Details: COMPLEX WAS CRYSTALLIZED AT PH 6.0 FROM 4-6% PEG, 20% ETHYLENE GLYCOL, 0.2 M NACL, 25 MM MGCL2 AND 2 MM AMP.
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlprotein1drop
34-6 %PEG33501reservoir
420 %ethylene glycol1reservoir
50.2 M1reservoirNaCl
625 mM1reservoirMgCl2
72 mMcAMP1reservoir
2DNA1drop1.3 molar excess

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorDetector: CCD / Date: Feb 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 22805 / % possible obs: 86.2 % / Biso Wilson estimate: 2.3 Å2 / Rsym value: 6.3 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 41.1
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Rmerge(I) obs: 0.411

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGP

1cgp


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.7 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.296 2012 9.9 %
obs0.237 20270 78.3 %
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-1.36 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1580 530 44 149 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.291.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it1.132
X-RAY DIFFRACTIONx_scangle_it1.772.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.383 173 9.1 %
Rwork0.332 1728 -
obs--59.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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