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Yorodumi- PDB-1yno: High Resolution Structure of Benzoylformate Decarboxylase from Ps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yno | ||||||
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Title | High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate | ||||||
Components | Benzoylformate decarboxylase | ||||||
Keywords | LYASE / CARBON-CARBON / DECARBOXYLASE / MANDELATE CATABOLISM / THIAMINE THIAZOLONE DIPHOSPHATE / HIGH RESOLUTION | ||||||
Function / homology | Function and homology information benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Bera, A.K. / Hasson, M.S. | ||||||
Citation | Journal: To be Published Title: High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate; Authors: Bera, A.K. / Anderson, N.L. / Hasson, M.S. #1: Journal: Biochemistry / Year: 1998 Title: The Crystal Structure of Benzoylformate Decarboxylase at 1.6 Angstrom Resolution: Diversity of Catalytic Residues in Thiamin Diphosphate-Dependent Enzymes Authors: Hasson, M.S. / Muscate, A. / Mcleish, M.J. / Polovnikova, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. #2: Journal: Biochemistry / Year: 2003 Title: Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase. Authors: Polovnikova, E.S. / Mcleish, M.J. / Sergienko, E.A. / Burgner, J.T. / Anderson, N.L. / Bera, A.K. / Jordan, F. / Kenyon, G.L. / Hasson, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yno.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yno.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1yno ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1yno | HTTPS FTP |
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-Related structure data
Related structure data | 1bfdS S: Starting model for refinement |
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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: 56271.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P20906, benzoylformate decarboxylase | ||||
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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | #4: Chemical | ChemComp-TZD / | #5: 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: 2.04 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 400,0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5) , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→99 Å / Num. all: 154670 / Num. obs: 154631 / % possible obs: 98.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.22→1.26 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.72 / % possible all: 86.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BFD Resolution: 1.22→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ? 5%
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.22→30 Å
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