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Yorodumi- PDB-5dgd: Benzoylformate decarboxylase F464I and A460V mutant from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dgd | |||||||||
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Title | Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida | |||||||||
Components | Benzoylformate decarboxylase | |||||||||
Keywords | LYASE / BENZOYLFORMATE DECARBOXYLASE / THIAMIN DIPHOSPHATE | |||||||||
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: 1.13 Å | |||||||||
Authors | Bera, A.K. / Hasson, M.S. | |||||||||
Citation | Journal: to be published Title: Benzoylformate decarboxylase F464I and A460V mutant from Pseudomonas putida Authors: Bera, A.K. / Hasson, M.S. #1: Journal: J.Am.Chem.Soc. / Year: 2007 Title: Mechanism-based inactivation of benzoylformate decarboxylase, a thiamin diphosphate-dependent enzyme. Authors: Bera, A.K. / Polovnikova, L.S. / Roestamadji, J. / Widlanski, T.S. / Kenyon, G.L. / McLeish, M.J. / 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 | 5dgd.cif.gz | 315.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dgd.ent.gz | 256 KB | Display | PDB format |
PDBx/mmJSON format | 5dgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/5dgd ftp://data.pdbj.org/pub/pdb/validation_reports/dg/5dgd | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 55940.156 Da / Num. of mol.: 1 / Mutation: A460V, F464I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: RF4738 / Gene: mdlC / Plasmid: PREP7 / Production host: Escherichia coli (E. coli) / References: UniProt: P20906, benzoylformate decarboxylase | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TPP / | #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: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24% (V/V) PEG 400, 0.15 M CACl2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→50 Å / Num. obs: 192537 / % possible obs: 96.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.29 |
Reflection shell | Resolution: 1.13→1.17 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 6.8 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BFD Resolution: 1.13→17.652 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.94 Å2 / Biso mean: 13.6474 Å2 / Biso min: 5.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.13→17.652 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 84.4958 Å / Origin y: 30.311 Å / Origin z: 157.3121 Å
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Refinement TLS group |
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