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Yorodumi- PDB-2fep: Structure of truncated CcpA in complex with P-Ser-HPr and Sulfate ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fep | ||||||
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Title | Structure of truncated CcpA in complex with P-Ser-HPr and Sulfate ions | ||||||
Components |
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Keywords | TRANSCRIPTION / CcpA / HPr / transcriptional regulator | ||||||
Function / homology | Function and homology information regulation of carbohydrate utilization / phosphoenolpyruvate-dependent sugar phosphotransferase system / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Chaptal, V. / Gueguen-Chaignon, V. / Poncet, S. / Lecampion, C. / Meyer, P. / Deutscher, J. / Galinier, A. / Nessler, S. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Structural analysis of B. subtilis CcpA effector binding site. Authors: Chaptal, V. / Gueguen-Chaignon, V. / Poncet, S. / Lecampion, C. / Meyer, P. / Deutscher, J. / Galinier, A. / Nessler, S. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fep.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fep.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/2fep ftp://data.pdbj.org/pub/pdb/validation_reports/fe/2fep | HTTPS FTP |
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-Related structure data
Related structure data | 1rzrS 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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Details | The biological assembly is a dimer generated from the monomer in the asymetric unit by a two fold crystallographic axis |
-Components
#1: Protein | Mass: 32183.639 Da / Num. of mol.: 1 / Fragment: residues 61-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ccpA, alsA, amyR, graR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25144 | ||
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#2: Protein | Mass: 9278.313 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ptsH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08877 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate 3.5M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004 |
Radiation | Monochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. all: 14948 / Num. obs: 14933 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34 Å2 / Rsym value: 0.091 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.45→2.58 Å / Mean I/σ(I) obs: 2 / Num. unique all: 2132 / Rsym value: 0.36 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1RZR Resolution: 2.45→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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