+Open data
-Basic information
Entry | Database: PDB / ID: 1i5z | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF CRP-CAMP AT 1.9 A | ||||||
Components | CATABOLITE GENE ACTIVATOR PROTEINCAMP receptor protein | ||||||
Keywords | DNA BINDING PROTEIN / CAMP receptor Protein (CRP) / Allostery / DNA binding Cyclic AMP / Transcription Regulation / CATABOLITE ACTIVATOR PROTEIN (CAP) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | White, M.A. / Lee, J.C. / Fox, R.O. | ||||||
Citation | Journal: To be Published Title: The effect of the D53H point mutation on the macroscopic motions of E. coli Cyclic AMP Receptor Protein Authors: White, M.A. / Liu, D. / Lin, S.-H. / Fox, R.O. / Lee, J.C. #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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i5z.cif.gz | 99 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i5z.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 1i5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i5z ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i5z | HTTPS FTP |
---|
-Related structure data
Related structure data | 1i6xC 3gap S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The Dimer is the biological unit |
-Components
#1: Protein | 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % |
---|---|
Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 7.8 Details: 100mM KCl, 1mM EDTA, 50mM TRIS, 35% Glycerol, cAMP, pH 7.8, LIQUID DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 25, 1998 / Details: MULTILAYER |
Radiation | Monochromator: MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 38852 / Num. obs: 38852 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1924 / Rsym value: 0.27 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GAP CRP DIMER 3gap Resolution: 1.9→46.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1679462.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.24 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.93 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|