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- PDB-3dhb: 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dhb | ||||||
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Title | 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at The Catalytic Metal Center | ||||||
![]() | N-Acyl Homoserine Lactone Hydrolase | ||||||
![]() | HYDROLASE / Zinc Bimetallohydrolase / Qourum Quenching / N-Acyl Homoserine Lactone / Product Complex / AHL Lactonase / General Acid / Catalytic Mechanism | ||||||
Function / homology | ![]() lactone catabolic process / acyl-L-homoserine-lactone lactonohydrolase activity / quorum-quenching N-acyl-homoserine lactonase / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, D. / Momb, J. / Thomas, P.W. / Moulin, A. / Petsko, G.A. / Fast, W. / Ringe, D. | ||||||
![]() | ![]() 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: ![]() Title: Mechanism of the Quorum-Quenching Lactonase (AiiA) from Bacillus thuringiensis: 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.6 KB | Display | ![]() |
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PDB format | ![]() | 103.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
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Full document | ![]() | 456 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dhaC ![]() 3dhcC ![]() 2a7mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Description: The fusion protein, maltose binding protein, was cut off using TEV protease resulting 4 extra residues at the N terminus in the sequence. But the extra residues are not seen in the structure. Gene: aiiA / Plasmid: pMAL / Production host: ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
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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, Methanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2006 / Details: K-B pair biomorph mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.64 Å / Num. obs: 49268 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4408 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2A7M Resolution: 1.4→18.79 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.009 / SU ML: 0.036 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.4 / ESU R: 0.065 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 20.668 Å2
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Refine analyze | Luzzati coordinate error obs: 0.053 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→18.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.437 Å / Total num. of bins used: 20
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