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Yorodumi- PDB-4k9n: Crystal Structure of the Ala460Ile mutant of Benzoylformate Decar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k9n | ||||||
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Title | Crystal Structure of the Ala460Ile mutant of Benzoylformate Decarboxylase from Pseudomonas putida | ||||||
Components | Benzoylformate decarboxylase | ||||||
Keywords | LYASE / Thiamine Diphosphate | ||||||
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: 1.7 Å | ||||||
Authors | Brodkin, H.R. / McLeish, M.J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Ala460Ile mutant of Benzoylformate Decarboxylase from Pseudomonas putida Authors: Brodkin, H.R. / Andrews, F.H. / Milne, A.C. / Petsko, G.A. / Ringe, D. / McLeish, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k9n.cif.gz | 436.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k9n.ent.gz | 353 KB | Display | PDB format |
PDBx/mmJSON format | 4k9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k9n_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4k9n_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4k9n_validation.xml.gz | 87.9 KB | Display | |
Data in CIF | 4k9n_validation.cif.gz | 131.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/4k9n ftp://data.pdbj.org/pub/pdb/validation_reports/k9/4k9n | HTTPS FTP |
-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
#1: Protein | Mass: 56817.094 Da / Num. of mol.: 4 / Mutation: A460I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlC / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P20906, benzoylformate decarboxylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TZD / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 22% PEG400, 150 mM calcium chloride, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2012 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.721 Å / Num. all: 206119 / Num. obs: 198992 / % possible obs: 92.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.9 / % possible all: 75.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BFD Resolution: 1.7→38.721 Å / SU ML: 0.34 / σ(F): 0.08 / Phase error: 19.88 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.037 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→38.721 Å
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Refine LS restraints |
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LS refinement shell |
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