[English] 日本語
Yorodumi- PDB-2cgp: CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cgp | ||||||
---|---|---|---|---|---|---|---|
Title | CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Passner, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cgp.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cgp.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2cgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/2cgp ftp://data.pdbj.org/pub/pdb/validation_reports/cg/2cgp | HTTPS FTP |
---|
-Related structure data
Related structure data | 1cgpS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3332.210 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
---|---|---|---|
#2: DNA chain | Mass: 4607.033 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: 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 | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 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
|
-Data collection
Diffraction | Mean temperature: 115 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 |
Detector | Detector: CCD / Date: Feb 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|