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- PDB-4g9e: Crystal structures of N-acyl homoserine lactonase AidH complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g9e | ||||||
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Title | Crystal structures of N-acyl homoserine lactonase AidH complexed with N-butanoyl homoserine | ||||||
![]() | Alpha/beta hydrolase fold protein | ||||||
![]() | HYDROLASE / alpha/beta-hydrolase fold / AHL-lactonase / AHL-binding | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liang, D.C. / Yan, X.X. / Gao, A. | ||||||
![]() | ![]() Title: High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism for N-acyl homoserine lactonase Authors: Gao, A. / Mei, G.Y. / Liu, S. / Wang, P. / Tang, Q. / Liu, Y.P. / Wen, H. / An, X.M. / Zhang, L.Q. / Yan, X.X. / Liang, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264.7 KB | Display | ![]() |
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PDB format | ![]() | 215.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.9 KB | Display | ![]() |
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Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g5xSC ![]() 4g8bC ![]() 4g8cC ![]() 4g8dC ![]() 4g9gC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30653.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG8000, 0.2M ammonium acetate, 0.01M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.088→21.29 Å / Num. obs: 179801 / % possible obs: 52.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 7.83 Å2 |
Reflection shell | Resolution: 1.09→1.12 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G5X Resolution: 1.088→21.29 Å / Occupancy max: 1 / Occupancy min: 0.07 / FOM work R set: 0.9246 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 13.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 148.829 Å2 / ksol: 0.544 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.21 Å2 / Biso mean: 15.5626 Å2 / Biso min: 4.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.088→21.29 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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