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- PDB-3bh3: Crystal structure of acetoacetate decarboxylase from Chromobacter... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bh3 | ||||||
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Title | Crystal structure of acetoacetate decarboxylase from Chromobacterium violaceum in complex with acetyl acetone Schiff base intermediate | ||||||
![]() | Acetoacetate decarboxylase | ||||||
![]() | LYASE / acetoacetate decarboxylase / Schiff base intermediate | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ho, M. / Allen, K.N. | ||||||
![]() | ![]() Title: The origin of the electrostatic perturbation in acetoacetate decarboxylase. Authors: Ho, M.C. / Menetret, J.F. / Tsuruta, H. / Allen, K.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.4 KB | Display | ![]() |
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PDB format | ![]() | 167.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.1 KB | Display | ![]() |
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Full document | ![]() | 471.7 KB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27329.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 30191 / IFO 12614 / JCM 1249 / NCIB 9131 / Gene: adc, CV_3520 / Plasmid: pET15b / Production host: ![]() ![]() #2: Chemical | ChemComp-PNH / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 0.5M Potassium phoshpate dibasic/Sodium phosphate monobasic, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 60919 / % possible obs: 99.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 37.137 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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