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Yorodumi- PDB-2nzv: Structural mechanism for the fine-tuning of CcpA function by the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nzv | ||||||
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Title | Structural mechanism for the fine-tuning of CcpA function by the small molecule effectors G6P and FBP | ||||||
Components |
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Keywords | TRANSCRIPTION / CCpA / HPrser46-p / CCR / fructose-bis-phosphate / adjunct corepressor / LacI-GalR | ||||||
Function / homology | Function and homology information phosphoenolpyruvate-dependent sugar phosphotransferase system / regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Schumacher, M.A. / Hillen, W. / Brennan, R.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Mechanism for the Fine-tuning of CcpA Function by The Small Molecule Effectors Glucose 6-Phosphate and Fructose 1,6-Bisphosphate. Authors: Schumacher, M.A. / Seidel, G. / Hillen, W. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nzv.cif.gz | 85 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nzv.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 2nzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nzv ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nzv | HTTPS FTP |
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-Related structure data
Related structure data | 2nzuSC 2oenC 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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Details | CCpA is a dimer and binds corepressor protein HPR-ser46p as monomer. |
-Components
#1: Protein | Mass: 30992.119 Da / Num. of mol.: 1 / Fragment: residues 53-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: ccpA / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46828 | ||
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#2: Protein | Mass: 9207.212 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: ptsH / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O69250 | ||
#3: Sugar | ChemComp-FBP / | ||
#4: Chemical | ChemComp-SO4 / #5: 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: 3.5 Å3/Da / Density % sol: 64.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammomium sulphate, 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: ALS / Beamline: 8.2.1 / Wavelength: 1.03 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 23, 2004 / Details: mirrors |
Radiation | Monochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 3→59.8 Å / Num. all: 11482 / Num. obs: 12099 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6 |
Reflection shell | Resolution: 3→3.19 Å / Redundancy: 2 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1000 / Rsym value: 0.333 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2nzu Resolution: 3→38.53 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2311774.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 89.4824 Å2 / ksol: 0.348082 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 93.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→38.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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