[English] 日本語
Yorodumi- PDB-2xua: Crystal structure of the enol-lactonase from Burkholderia xenovor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xua | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the enol-lactonase from Burkholderia xenovorans LB400 | ||||||
Components | 3-OXOADIPATE ENOL-LACTONASE | ||||||
Keywords | HYDROLASE / CATECHOL METABOLISM | ||||||
Function / homology | Function and homology information 3-oxoadipate enol-lactonase / 3-oxoadipate enol-lactonase activity / beta-ketoadipate pathway Similarity search - Function | ||||||
Biological species | BURKHOLDERIA XENOVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Bains, J. / Kaufman, L. / Farnell, B. / Boulanger, M.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: A Product Analog Bound Form of 3-Oxoadipate-Enol- Lactonase (Pcad) Reveals a Multifunctional Role for the Divergent CAP Domain. Authors: Bains, J. / Kaufman, L. / Farnell, B. / Boulanger, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xua.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xua.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xua_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2xua_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 2xua_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 2xua_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/2xua ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xua | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29182.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA XENOVORANS (bacteria) / Strain: LB400 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q13KT2, 3-oxoadipate enol-lactonase #2: Chemical | ChemComp-SHF / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→36 Å / Num. obs: 36592 / % possible obs: 93.4 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 |
-Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→36.26 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.713 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.908 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→36.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|