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- PDB-6j3d: Crystal structure of acetolactate decarboxylase from Bacillus sub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j3d | ||||||
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Title | Crystal structure of acetolactate decarboxylase from Bacillus subtilis subspecies spizizenii in space group P21212 | ||||||
![]() | Alpha-acetolactate decarboxylase | ||||||
![]() | LYASE / enzyme / decarboxylase | ||||||
Function / homology | ![]() acetolactate decarboxylase / acetoin biosynthetic process / acetolactate decarboxylase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoon, S.I. | ||||||
![]() | ![]() Title: Crystal structure of alpha-acetolactate decarboxylase from Bacillus subtilis subspecies spizizeni. Authors: Eom, J. / Oh, H.B. / Yoon, S.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202 KB | Display | ![]() |
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PDB format | ![]() | 160.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.8 KB | Display | ![]() |
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Full document | ![]() | 434.5 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bt4S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 29308.799 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 23059 / NRRL B-14472 / W23 / Gene: alsD, BSUW23_17695 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 18% PEG 4000, 0.08M ammonium sulfate, 0.1M sodium acetate, pH 4.5, 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 58087 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 44.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 7.2 / Num. unique obs: 2833 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 4BT4 Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.303 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.09 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.599 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→30 Å
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Refine LS restraints |
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