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Yorodumi- PDB-3rdi: Domain-domain flexibility leads to allostery within the camp rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rdi | ||||||
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Title | Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) | ||||||
Components | Catabolite gene activator | ||||||
Keywords | TRANSCRIPTION REGULATOR / CAMP RECEPTOR PROTEIN (CRP) / ALLOSTERY / DNA BINDING CYCLIC AMP / CATABOLITE ACTIVATOR PROTEIN (CAP) / DNA BINDING PROTEIN | ||||||
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: 2.95 Å | ||||||
Authors | Knapp, J. / White, M.A. / Lee, J.C. | ||||||
Citation | Journal: To be Published Title: Domain-Domain Flexibility Leads to Allostery within the Cam Receptor Protein (Crp) Authors: Knapp, J. / White, M.A. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rdi.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rdi.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/3rdi ftp://data.pdbj.org/pub/pdb/validation_reports/rd/3rdi | HTTPS FTP |
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-Related structure data
Related structure data | 3rouC 3rpqC 3rypC 3ryrC 1il5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 23732.537 Da / Num. of mol.: 2 / Mutation: S63F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3357, cap, crp, csm, JW5702 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ACJ8 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% ETHANOL, 100MM TRIS, 3MM CAMP, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 85 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 9, 2007 / Details: CONFOCAL |
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: 2.95→40 Å / Num. all: 9807 / Num. obs: 9807 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 134.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.45 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IL5 Resolution: 2.95→34.65 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1670547.31 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: 2 NCS GROUPS
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Displacement parameters | Biso mean: 74.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→34.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 0 Å2 / Rms dev position: 0 Å / Weight Biso : 2 / Weight position: 2000
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LS refinement shell | Resolution: 2.95→3 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 20
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Xplor file |
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