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- PDB-4alb: Structure of Phenolic Acid Decarboxylase from Bacillus subtilis: ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4alb | ||||||
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Title | Structure of Phenolic Acid Decarboxylase from Bacillus subtilis: Tyr19Ala mutant in complex with coumaric acid | ||||||
![]() | PHENOLIC ACID DECARBOXYLASE PADC | ||||||
![]() | LYASE / LIPOCALIN OLD / CINNAMATE | ||||||
Function / homology | ![]() phenacrylate decarboxylase / carboxy-lyase activity / : / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frank, A. / Eborall, W. / Hyde, R. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
![]() | ![]() Title: Mutational Analysis of Phenolic Acid Decarboxylase from Bacillus Subtilis (Bspad), which Converts Bio-Derived Phenolic Acids to Styrene Derivatives Authors: Frank, A. / Eborall, W. / Hyde, R. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.7 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 465.5 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p8gS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 19008.393 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O07006, Lyases; Carbon-carbon lyases; Carboxy-lyases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 9 Details: 0.2 M KSCN, 17% (W/V) PEG 1000, 17% (W/V) PEG 8000, IN 0.1 M TRIS/HCL BUFFER AT PH 9. 15 MM COUMARIC ACID. PROTEIN AT 20 MG PER ML |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→53.6 Å / Num. obs: 12362 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 3.02→3.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 3.3 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB MODEL 2P8G Resolution: 3.03→92.85 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 17.885 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 44.643 Å2
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Refinement step | Cycle: LAST / Resolution: 3.03→92.85 Å
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Refine LS restraints |
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