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Yorodumi- PDB-3duv: Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3duv | ||||||
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Title | Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the-configuration | ||||||
Components | 3-deoxy-manno-octulosonate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / CMP-KDO synthetase / 3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate / kdsB / Cytoplasm / Lipopolysaccharide biosynthesis / Nucleotidyltransferase | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Yoon, H.J. / Ku, M.J. / Mikami, B. / Suh, S.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the beta-configuration. Authors: Yoon, H.J. / Ku, M.J. / Mikami, B. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3duv.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3duv.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 3duv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/3duv ftp://data.pdbj.org/pub/pdb/validation_reports/du/3duv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29593.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: kdsB / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) References: UniProt: P44490, 3-deoxy-manno-octulosonate cytidylyltransferase #2: Sugar | #3: Chemical | ChemComp-P4C / | #4: 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: 1.95 Å3/Da / Density % sol: 37.08 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 100mM sodium citrate (pH5.6), 50mM ammonium acetate, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 24031 / % possible obs: 93.9 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.133 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.279 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.608 / ESU R Free: 0.271 / 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 max: 96.59 Å2 / Biso mean: 28.969 Å2 / Biso min: 3.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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