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Open data
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Basic information
Entry | Database: PDB / ID: 1bfd | ||||||
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Title | BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA | ||||||
![]() | BENZOYLFORMATE DECARBOXYLASE | ||||||
![]() | LYASE / CARBON-CARBON / DECARBOXYLASE / MANDELATE CATABOLISM / THIAMIN DIPHOSPHATE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hasson, M.S. / Muscate, A. / Mcleish, M.J. / Polovnikova, L.S. / Gerlt, J.A. / Kenyon, G.L. / Petsko, G.A. / Ringe, D. | ||||||
![]() | ![]() Title: The crystal structure of benzoylformate decarboxylase at 1.6 A 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. #1: ![]() Title: Purification and Crystallization of Benzoylformate Decarboxylase Authors: Hasson, M.S. / Muscate, A. / Henehan, G.T. / Guidinger, P.F. / Petsko, G.A. / Ringe, D. / Kenyon, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.4 KB | Display | ![]() |
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PDB format | ![]() | 92 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 736.3 KB | Display | ![]() |
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Full document | ![]() | 738.2 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: 56402.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-TPP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE BY HANGING-DROP VAPOR DIFFUSION AGAINST A WELL SOLUTION OF 22% (V/V) POLYETHYLENE GLYCOL WITH AN AVERAGE MOLECULAR WEIGHT OF 400 KDA (PEG 400), 0.15 M CACL2, 0.5% (V/V) MPD, 0.1 M TRISCL (PH 8.5). DROPS CONTAINED EQUAL VOLUMES (2 MICROL) OF WELL SOLUTION AND PURIFIED BENZOYLFORMATE DECARBOXYLASE [10 MG/ML IN 0.1 MM MGCL2, 0.2 MM TDP, 25 MM NAHEPES (PH 7.0)]., vapor diffusion - hanging drop PH range: 7.0-8.5 / Temp details: room temp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.6 Å / Num. obs: 59179 / % possible obs: 81 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.6→1.7 Å / Mean I/σ(I) obs: 2.2 / % possible all: 32 |
Reflection | *PLUS Num. measured all: 217078 |
Reflection shell | *PLUS % possible obs: 32 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: VAL 524 IS THE LAST RESIDUE FOR WHICH INTERPRETABLE ELECTRON DENSITY WAS PRESENT.
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Displacement parameters | Biso mean: 18.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 59179 / Rfactor obs: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.275 |