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Yorodumi- PDB-6m2y: Crystal structure of a formolase, BFD variant M6 from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6m2y | ||||||
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Title | Crystal structure of a formolase, BFD variant M6 from Pseudomonas putida | ||||||
Components | Benzoylformate decarboxylase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / decarboxylases | ||||||
Function / homology | Function and homology information benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / acetolactate synthase activity / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wei, H.L. / Liu, W.D. / Li, T.Z. / Zhu, L.L. | ||||||
Citation | Journal: Green Chem / Year: 2020 Title: Totally atom-economical synthesis of lactic acid from formaldehyde: combined bio-carboligation and chemo-rearrangement without the isolation of intermediate. Authors: Li, T. / Tang, Z. / Wei, H. / Tan, Z. / Liu, P. / Li, J. / Zheng, Y. / Lin, J. / Liu, W. / Jiang, H. / Liu, H. / Zhu, L. / Ma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m2y.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m2y.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 6m2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/6m2y ftp://data.pdbj.org/pub/pdb/validation_reports/m2/6m2y | HTTPS FTP |
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-Related structure data
Related structure data | 6m2zC 6a50S 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: 56495.848 Da / Num. of mol.: 1 / Mutation: S26F, W86R, N87T, L109S, L110E, H281Y, A460M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 trixb(DE3) / References: UniProt: P20906, benzoylformate decarboxylase |
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#2: Chemical | ChemComp-TPP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % / Mosaicity: 0.579 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M acetate pH 4.5, 0.2 M NaCl,40% (v/v) PEG-300 |
-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 PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.06→25 Å / Num. obs: 39009 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.072 / Rrim(I) all: 0.255 / Χ2: 0.724 / Net I/σ(I): 3.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6A50 Resolution: 2.1→24.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.919 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 82.05 Å2 / Biso mean: 16.587 Å2 / Biso min: 3.89 Å2
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Refinement step | Cycle: final / Resolution: 2.1→24.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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