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- PDB-4za7: Structure of A. niger Fdc1 in complex with alpha-methyl cinnamic acid -
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Open data
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Basic information
Entry | Database: PDB / ID: 4za7 | ||||||
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Title | Structure of A. niger Fdc1 in complex with alpha-methyl cinnamic acid | ||||||
![]() | Fdc1 | ||||||
![]() | LYASE / (de)carboxylase / prenylated flavin binding / UbiD-type enzyme | ||||||
Function / homology | ![]() styrene metabolic process / aromatic amino acid family catabolic process / phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / manganese ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Payne, K.A.P. / Leys, D. | ||||||
![]() | ![]() Title: New cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Authors: Payne, K.A. / White, M.D. / Fisher, K. / Khara, B. / Bailey, S.S. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Beveridge, R. / Barran, P. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.7 KB | Display | ![]() |
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PDB format | ![]() | 188.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4za4SC ![]() 4za5C ![]() 4za8C ![]() 4za9C ![]() 4zaaC ![]() 4zabC ![]() 4zacC ![]() 4zadC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56335.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A2QHE5, 4-hydroxybenzoate decarboxylase |
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-Non-polymers , 6 types, 471 molecules ![](data/chem/img/4LU.gif)
![](data/chem/img/FZZ.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/4LV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FZZ.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/4LV.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-4LU / | ||||
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#3: Chemical | ChemComp-FZZ / | ||||
#4: Chemical | ChemComp-MN / | ||||
#5: Chemical | #6: Chemical | ChemComp-4LV / ( | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→87.7 Å / Num. obs: 203456 / % possible obs: 98 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZA4 Resolution: 1.1→30.05 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.768 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.024 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.253 Å2
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Refinement step | Cycle: 1 / Resolution: 1.1→30.05 Å
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Refine LS restraints |
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