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Yorodumi- PDB-3dhc: 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dhc | ||||||
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Title | 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to The catalytic Metal Center | ||||||
Components | N-Acyl Homoserine Lactone Hydrolase | ||||||
Keywords | HYDROLASE / Zinc Bimetallohydrolase / Qourum Quenching / N-Acyl Homocysteine Thiolactone / Product Complex / AHL Lactonase / General Acid / Catalytic Mechanism | ||||||
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: 1.3 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 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dhc.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dhc.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dhc_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 3dhc_full_validation.pdf.gz | 458.8 KB | Display | |
Data in XML | 3dhc_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 3dhc_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dhc ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dhc | HTTPS FTP |
-Related structure data
Related structure data | 3dhaC 3dhbC 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: TEV protease was used to cut off the fusion protein MBP resulting in 4 extra residues at the N terminus. The extra residues are not observed in the structure 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-CYK / | #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: 41.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Glycerol, Tris-HCl, MgCl2, N-Hexanoyl-L-Homocysteine Thiolactone, Methanol, 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: 0.97934 Å |
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: 1.3→50 Å / Num. all: 60162 / Num. obs: 56793 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.1 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A7M Resolution: 1.3→23.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.615 / SU ML: 0.03 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze | Luzzati coordinate error obs: 0.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→23.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.33 Å / Total num. of bins used: 20
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