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Yorodumi- PDB-3cra: Crystal Structure of Escherichia coli MazG, the Regulator of Nutr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cra | ||||||
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Title | Crystal Structure of Escherichia coli MazG, the Regulator of Nutritional Stress Response | ||||||
Components | Protein mazG | ||||||
Keywords | HYDROLASE / Tandem-repeat domain | ||||||
Function / homology | Function and homology information ATP diphosphatase / TTP catabolic process / UTP catabolic process / dTTP catabolic process / dATP catabolic process / nucleoside triphosphate diphosphatase activity / dGTP catabolic process / ATP diphosphatase activity / dUTP catabolic process / cellular response to starvation ...ATP diphosphatase / TTP catabolic process / UTP catabolic process / dTTP catabolic process / dATP catabolic process / nucleoside triphosphate diphosphatase activity / dGTP catabolic process / ATP diphosphatase activity / dUTP catabolic process / cellular response to starvation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Lee, S. / Kim, M.H. / Kang, B.S. / Kim, J.S. / Kim, Y.G. / Kim, K.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response. Authors: Lee, S. / Kim, M.H. / Kang, B.S. / Kim, J.S. / Kim, G.H. / Kim, Y.G. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cra.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cra.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/3cra ftp://data.pdbj.org/pub/pdb/validation_reports/cr/3cra | HTTPS FTP |
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-Related 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: 30644.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: mazG / Plasmid: pPROEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B832 / References: UniProt: P0AEY3 #2: 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: 2.43 Å3/Da / Density % sol: 49.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M trisodium citrate(pH 5.5), 0.2M ammonium acetate, 20% polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2006 |
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23985 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 41095 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique all: 41095 / Rsym value: 0.324 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→28.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.705 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.781 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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