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Yorodumi- PDB-1eyr: Structure of a sialic acid activating synthetase, CMP acylneurami... -
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-Basic information
Entry | Database: PDB / ID: 1eyr | ||||||
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Title | Structure of a sialic acid activating synthetase, CMP acylneuraminate synthetase in the presence and absence of CDP | ||||||
Components | CMP-N-ACETYLNEURAMINIC ACID SYNTHETASE | ||||||
Keywords | TRANSFERASE / SYNTHETASE / SIALIC ACID / CDP / ACYLNEURAMINATE | ||||||
Function / homology | Function and homology information N-acylneuraminate cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Mosimann, S.C. / Gilbert, M. / Dombrowski, D. / Wakarchuk, W. / Strynadka, N.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structure of a sialic acid-activating synthetase, CMP-acylneuraminate synthetase in the presence and absence of CDP. Authors: Mosimann, S.C. / Gilbert, M. / Dombroswki, D. / To, R. / Wakarchuk, W. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eyr.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eyr.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 1eyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eyr ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eyr | 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: 25154.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Neisseria meningitidis (bacteria) References: UniProt: P0A0Z8, N-acylneuraminate cytidylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.71 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: PEG-2000, magnesium sulfate, ethanol, Tris buffer, CDP, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 15.7 Å2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 21889 / % possible obs: 87.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.061 |
-Processing
Software |
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Refinement | Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1598881.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE TOPOLOGY AND PARAMETER FILE CDPW.TOP AND CDPW.PAR ARE CYTOSINE-5'-DIPHOSPHATE TOPOLOGY PARAMETER FILES WITH AN ADDITIONAL WATER. THE FOLLOWING RESIDUES HAVE BEEN MODELED AS ALA: LYS( B 125 ), GLN( B 146 ).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.19 Å2 / ksol: 0.3424 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rfree: 0.247 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.337 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.243 |