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Yorodumi- PDB-7dam: Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dam | ||||||
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Title | Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae | ||||||
Components | ATP phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Adenosine triphosphate phosphoribosyltransferase | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae serotype O1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Pal, R.K. / Gourinath, S. / Biswal, B.K. | ||||||
Citation | Journal: To Be Published Title: Adenosine triphosphate phosphoribosyltransferase from Vibrio cholerae Authors: Pal, R.K. / Gourinath, S. / Biswal, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dam.cif.gz | 112.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dam.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7dam ftp://data.pdbj.org/pub/pdb/validation_reports/da/7dam | HTTPS FTP |
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-Related structure data
Related structure data | 1h3dS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 0 / Auth seq-ID: 10 - 303 / Label seq-ID: 16 - 309
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-Components
#1: Protein | Mass: 34579.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain M66-2) (bacteria) Strain: M66-2 / Gene: hisG, VCM66_1088 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3LU29, ATP phosphoribosyltransferase #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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: 0.1 M Sodium acetate trihydrate pH 4.6 2.0 M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 17005 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.995 / Net I/σ(I): 14.54 | |||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Num. unique obs: 1706 / CC1/2: 0.451 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H3D Resolution: 2.7→36.67 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.724 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 134.49 Å2 / Biso mean: 58.298 Å2 / Biso min: 38.28 Å2
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Refinement step | Cycle: final / Resolution: 2.7→36.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 6192 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.705→2.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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