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Yorodumi- PDB-6inb: Crystal structure of an acetolactate decarboxylase from Klebsiell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6inb | ||||||
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Title | Crystal structure of an acetolactate decarboxylase from Klebsiella pneumoniae | ||||||
Components | Alpha-acetolactate decarboxylase | ||||||
Keywords | UNKNOWN FUNCTION / Acetolactate decarboxylase | ||||||
Function / homology | Function and homology information acetolactate decarboxylase / acetoin biosynthetic process / acetolactate decarboxylase activity Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wu, W. / Zhang, Q. / Bartlam, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural characterization of an acetolactate decarboxylase from Klebsiella pneumoniae Authors: Wu, W. / Zhao, Q. / Che, S. / Jia, H. / Liang, H. / Zhang, H. / Liu, R. / Zhang, Q. / Bartlam, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6inb.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6inb.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 6inb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/6inb ftp://data.pdbj.org/pub/pdb/validation_reports/in/6inb | HTTPS FTP |
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-Related structure data
Related structure data | 6incC 4bt2S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29226.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: budA, BN49_3166 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W9BHF3, acetolactate decarboxylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: 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: 1.8 Å3/Da / Density % sol: 31.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG-3000, 0.1M citrate, pH 5.5 and 12% w/v Polyethylene glycol 3,350, 0.1M sodium malonate, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 20250 / % possible obs: 100 % / Redundancy: 19 % / Rpim(I) all: 0.021 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 15 % / Mean I/σ(I) obs: 9.5 / Num. unique obs: 999 / Rpim(I) all: 0.09 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BT2 Resolution: 1.8→47.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.644 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.88 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→47.87 Å
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Refine LS restraints |
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