[English] 日本語
Yorodumi- PDB-1sb8: Crystal structure of Pseudomonas aeruginosa UDP-N-acetylglucosami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sb8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Pseudomonas aeruginosa UDP-N-acetylglucosamine 4-epimerase complexed with UDP-N-acetylgalactosamine | ||||||
Components | wbpP | ||||||
Keywords | ISOMERASE / WbpP / epimerase / 4-epimerase / UDP-GalNAc / UDP-GlcNAc / SDR / GalE / NAD / SYK / pseudomonas aeruginosa / UDP / N-acetylglucosamine / N-acetylgalactosamine / UDP-Glc | ||||||
Function / homology | Function and homology information UDP-L-rhamnose synthase activity / UDP-glucose 4,6-dehydratase activity / UDP-rhamnose biosynthetic process / dTDP-glucose 4,6-dehydratase activity / flavonol biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ishiyama, N. / Creuzenet, C. / Lam, J.S. / Berghuis, A.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure of WbpP, a Genuine UDP-N-acetylglucosamine 4-Epimerase from Pseudomonas aeruginosa: SUBSTRATE SPECIFICITY IN UDP-HEXOSE 4-EPIMERASES. Authors: Ishiyama, N. / Creuzenet, C. / Lam, J.S. / Berghuis, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sb8.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sb8.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 1sb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sb8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1sb8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1sb8_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1sb8_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/1sb8 ftp://data.pdbj.org/pub/pdb/validation_reports/sb/1sb8 | HTTPS FTP |
-Related structure data
Related structure data | 1sb9SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operation: x, -y, -z+1 |
-Components
#1: Protein | Mass: 39080.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: wbpP / Plasmid: pET23 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS References: GenBank: 20560072, UniProt: Q8KN66*PLUS, UDP-N-acetylglucosamine 4-epimerase |
---|---|
#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-UD2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 52.9 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 600, phosphate-citrate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.25 Å / Num. all: 24082 / Num. obs: 23213 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2271 / Rsym value: 0.328 / % possible all: 89.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: partially refined model of PDB entry 1SB9 Resolution: 2.1→41.25 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 145620.51 / Data cutoff high rms absF: 145620.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.1887 Å2 / ksol: 0.392563 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.25 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|