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Yorodumi- PDB-4yfb: Structure of N-acylhomoserine lactone acylase MacQ in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yfb | ||||||
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Title | Structure of N-acylhomoserine lactone acylase MacQ in complex with phenylacetic acid | ||||||
Components | (Protein related to penicillin ...) 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: 1.75 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yfb.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4yfb.ent.gz | 969.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/4yfb ftp://data.pdbj.org/pub/pdb/validation_reports/yf/4yfb | HTTPS FTP |
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-Related structure data
Related structure data | 4yf9C 4yfaC 5c9iC 2wybS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein related to penicillin ... , 3 types, 12 molecules ADGJBEHKCFIL
#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 |
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-Non-polymers , 3 types, 2409 molecules
#4: Chemical | ChemComp-PAC / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % |
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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 |
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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: 1.75→50 Å / Num. obs: 319483 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.29 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.18 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code, 2WYB Resolution: 1.75→25.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.815 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 21.298 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→25.14 Å
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Refine LS restraints |
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