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Yorodumi- PDB-3dha: An Ultral High Resolution Structure of N-Acyl Homoserine Lactone ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dha | ||||||
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Title | An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site | ||||||
Components | N-Acyl Homoserine Lactone Hydrolase | ||||||
Keywords | HYDROLASE / Zinc Bimetallohydrolase / Quorum Quenching / N-Acyl Homoserine lactone / Alternative Binding Site / Product Complex / AHL Lactonase | ||||||
Function / homology | Function and homology information lactone catabolic process / acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus thuringiensis serovar kurstaki (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Liu, D. / Momb, J. / Thomas, P.W. / Moulin, A. / Petsko, G.A. / Fast, W. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures. Authors: Liu, D. / Momb, J. / Thomas, P.W. / Moulin, A. / Petsko, G.A. / Fast, W. / Ringe, D. #1: Journal: To be Published Title: Mechanism of the Quorum-quenching Lactonase (AiiA) from Bacillus thuringensis: 2. Substrate Modeling and Active Site Mutations Authors: Momb, J. / Wang, C. / Liu, D. / Thomas, P.W. / Petsko, G.A. / Guo, H. / Ringe, D. / Fast, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dha.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dha.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 3dha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dha_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 3dha_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 3dha_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3dha_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dha ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dha | HTTPS FTP |
-Related structure data
Related structure data | 3dhbC 3dhcC 2a7mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28664.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria) Description: The fusion protein, maltose binding protein, was cut off before crystallization using TEV protease resulting in 4 extra residues at the N terminus. Gene: aiiA / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7B8B9, UniProt: P0CJ63*PLUS, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-C6L / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Glycerol, Tris-HCl, PEG4000, MgCl2, N-hexanoyl-L-homoserine lactone, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9184 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2006 / Details: K-B pair of biomorph mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. obs: 141032 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 0.95→0.98 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2 / Num. unique all: 9081 / % possible all: 61.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A7M Resolution: 0.95→45 Å / Num. parameters: 22638 / Num. restraintsaints: 28771 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.0565
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Displacement parameters | Biso mean: 21.8 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.037 Å / Num. disordered residues: 18 / Occupancy sum hydrogen: 1951 / Occupancy sum non hydrogen: 2406.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.98 Å /
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