[English] 日本語
Yorodumi- PDB-2wyd: The quorum quenching N-acyl homoserine lactone acylase PvdQ in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wyd | ||||||
---|---|---|---|---|---|---|---|
Title | The quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with dodecanoic acid | ||||||
Components |
| ||||||
Keywords | HYDROLASE / ZYMOGEN / PERIPLASM | ||||||
Function / homology | Function and homology information acyl-homoserine-lactone acylase / : / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / quorum sensing / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / : / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / quorum sensing / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Bokhove, M. / Nadal Jimenez, P. / Quax, W.J. / Dijkstra, B.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: The Quorum-Quenching N-Acyl Homoserine Lactone Acylase Pvdq is an Ntn-Hydrolase with an Unusual Substrate-Binding Pocket Authors: Bokhove, M. / Nadal Jimenez, P. / Quax, W.J. / Dijkstra, B.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2wyd.cif.gz | 156.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2wyd.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wyd ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyd | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18592.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 SUBSTR. DH10B References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 60489.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 SUBSTR. DH10B References: UniProt: Q9I194, acyl-homoserine-lactone acylase | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE |
---|---|
Crystal grow | pH: 9 / Details: 24% PEG 6000, 100 MM BICINE PH 9.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.13 Å / Num. obs: 73345 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.24 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.63 / % possible all: 88.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→39.129 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.684 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.112 / 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: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.768 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→39.129 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|