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Yorodumi- PDB-3ryp: Domain-domain flexibility leads to allostery within the camp rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ryp | ||||||
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Title | Domain-domain flexibility leads to allostery within the camp receptor protein (CRP) | ||||||
Components | Catabolite gene activator | ||||||
Keywords | DNA BINDING PROTEIN / CAMP RECEPTOR PROTEIN (CRP) / ALLOSTERY / DNA BINDING CYCLIC AMP / TRANSCRIPTION REGULATOR / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 refined 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 | 3ryp.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ryp.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ryp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ryp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3ryp_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ryp_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 3ryp_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/3ryp ftp://data.pdbj.org/pub/pdb/validation_reports/ry/3ryp | HTTPS FTP |
-Related structure data
Related structure data | 3rdiC 3rouC 3rpqC 3ryrC 1il5S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 23672.439 Da / Num. of mol.: 2 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: Chemical | #4: 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, hanging drop / pH: 6.8 Details: 10% ETHANOL, 100MM PHOSPHATE, PH 6.8, 3MM CAMP, 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2007 | |||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→40 Å / Num. all: 60457 / Num. obs: 60457 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 37.6 | |||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.493 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IL5 Resolution: 1.6→38.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1374067.21 / Data cutoff low absF: 0 / Isotropic thermal model: variable / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.3382 Å2 / ksol: 0.377403 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→38.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.63 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
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Xplor file |
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