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Yorodumi- PDB-6inc: Crystal structure of an acetolactate decarboxylase from Klebsiell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6inc | ||||||
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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: 1.604 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 | 6inc.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6inc.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 6inc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/6inc ftp://data.pdbj.org/pub/pdb/validation_reports/in/6inc | HTTPS FTP |
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-Related structure data
Related structure data | 6inbC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 264 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: 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: 1.79 Å3/Da / Density % sol: 31.41 % |
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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 respectively |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 28357 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rpim(I) all: 0.034 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1389 / Rpim(I) all: 0.165 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BT2 Resolution: 1.604→27.576 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.604→27.576 Å
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Refine LS restraints |
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LS refinement shell |
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