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- PDB-1g6n: 2.1 ANGSTROM STRUCTURE OF CAP-CAMP -

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Basic information

Entry
Database: PDB / ID: 1g6n
Title2.1 ANGSTROM STRUCTURE OF CAP-CAMP
ComponentsCATABOLITE GENE ACTIVATOR PROTEIN
KeywordsDNA BINDING PROTEIN / Catabolite activator protein (CAP) / cAMP receptor protein (CRP) / transcription / allostery / cyclic AMP / cAMP
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-binding transcriptional dual regulator CRP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPassner, J.M. / Schultz, S.C. / Steitz, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution.
Authors: Passner, J.M. / Schultz, S.C. / Steitz, T.A.
#1: Journal: J.MOL.BIOL. / Year: 1987
Title: Structure of a complex of catabolite gene activator protein and cyclic AMP at 2.5 A resolution
Authors: Weber, I.T. / Steitz, T.A.
History
DepositionNov 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2000Provider: repository / Type: Initial release
SupersessionDec 20, 2000ID: 3GAP
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: CATABOLITE GENE ACTIVATOR PROTEIN
B: CATABOLITE GENE ACTIVATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0034
Polymers47,3452
Non-polymers6582
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-39 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.8, 95.6, 105.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23672.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PHAT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P0ACJ8
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7.5
Details: 0.1mM cAMP, 0.2M sodium chloride, 5mM Tris, O.1mM EDTA, 2mM DTT, .02% sodium azide, pH 7.5, MICRODIALYSIS, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein11
25 mMTris-HCl11
30.2 M11NaCl
40.1 mMEDTA11
50.02 %(w/v)sodium azide11
60.1 mMcAMP12
75 mMTris-HCl12
850 mM12NaCl
90.1 mMEDTA12
102 mMdithiothreitol12
110.02 %(w/v)sodium azide12
122 mMdithiothreitol11
130-30 %ethylene glycol12

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Data collection

DiffractionMean temperature: 253 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: UCSD MARK III / Detector: AREA DETECTOR / Date: Mar 1, 1990
RadiationMonochromator: GRAPHITE + NICKLE FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→25 Å / Num. obs: 31208 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.0525 / Net I/σ(I): 14.3
Reflection shellResolution: 1.97→2.12 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.37
Reflection
*PLUS
Num. measured all: 90177
Reflection shell
*PLUS
Num. unique obs: 4506 / Num. measured obs: 8697

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
UCSD-systemdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GAP

3gap
PDB Unreleased entry


Resolution: 2.1→12 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.207 --
all0.231 26730 -
obs0.207 23393 82.9 %
Rfree-0 -
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 44 115 3329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.008

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