[English] 日本語
Yorodumi- PDB-3ojl: Native structure of the UDP-N-acetyl-mannosamine dehydrogenase Ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ojl | ||||||
---|---|---|---|---|---|---|---|
Title | Native structure of the UDP-N-acetyl-mannosamine dehydrogenase Cap5O from Staphylococcus aureus | ||||||
Components | Cap5O | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / binary complex / cofactor NAD / dimer / oxidoreduction | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / polysaccharide biosynthetic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Nessler, S. / Gruszczyk, J. / Olivares-Illana, V. / Meyer, P. / Morera, S. / Grangeasse, C. / Fleurie, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure Analysis of the Staphylococcus aureus UDP-N-acetyl-mannosamine Dehydrogenase Cap5O Involved in Capsular Polysaccharide Biosynthesis. Authors: Gruszczyk, J. / Fleurie, A. / Olivares-Illana, V. / Bechet, E. / Zanella-Cleon, I. / Morera, S. / Meyer, P. / Pompidor, G. / Kahn, R. / Grangeasse, C. / Nessler, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ojl.cif.gz | 174.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ojl.ent.gz | 138.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ojl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ojl_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ojl_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3ojl_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 3ojl_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/3ojl ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3ojl | HTTPS FTP |
-Related structure data
Related structure data | 3ojoSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48173.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Reynolds and Newman / Gene: cap5O / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P95708 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mg/ml CAP5O, 10 mM NAD, 24% PEG 4000, 0.2M sodium acetate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 7, 2007 |
Radiation | Monochromator: toroidal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 22365 / Num. obs: 22365 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 79.09 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.117 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.746 / % possible all: 89.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OJO Resolution: 2.8→29.12 Å / Cor.coef. Fo:Fc: 0.9168 / Cor.coef. Fo:Fc free: 0.8942 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.03 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.398 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.94 Å / Total num. of bins used: 11
|