[English] 日本語
Yorodumi- PDB-4yfa: Structure of N-acylhomoserine lactone acylase MacQ in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yfa | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of N-acylhomoserine lactone acylase MacQ in complex with decanoic acid | ||||||
Components | (Protein related to penicillin acylase) x 3 | ||||||
Keywords | HYDROLASE / Acylase / product complex / Ntn-hydrolase fold | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Acidovorax sp. MR-S7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Yasutake, Y. / Kusada, H. / Kimura, N. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Bifunctional quorum-quenching and antibiotic-acylase MacQ forms a 170-kDa capsule-shaped molecule containing spacer polypeptides Authors: Yasutake, Y. / Kusada, H. / Ebuchi, T. / Hanada, S. / Kamagata, Y. / Tamura, T. / Kimura, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yfa.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yfa.ent.gz | 958.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yfa_validation.pdf.gz | 535.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4yfa_full_validation.pdf.gz | 565.8 KB | Display | |
Data in XML | 4yfa_validation.xml.gz | 109.1 KB | Display | |
Data in CIF | 4yfa_validation.cif.gz | 153.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfa ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfa | HTTPS FTP |
-Related structure data
Related structure data | 4yf9C 4yfbC 5c9iC 2wybS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19231.340 Da / Num. of mol.: 4 / Fragment: alpha-chain, UNP residues 29-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1VBK6 #2: Protein/peptide | Mass: 2653.900 Da / Num. of mol.: 4 / Fragment: spacer peptide, UNP residues 207-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1VBK6 #3: Protein | Mass: 62611.613 Da / Num. of mol.: 4 / Fragment: beta-chain, UNP residues 234-806 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidovorax sp. MR-S7 (bacteria) / Gene: AVS7_00617 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A1VBK6 #4: Chemical | ChemComp-DKA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.78 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, calcium acetate, PEG 3350 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 159207 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.3 / % possible all: 97.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WYB Resolution: 2.2→38.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.197 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 45.924 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|