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Yorodumi- PDB-6r3g: Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r3g | |||||||||
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Title | Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the covalent adduct formed between prFMN cofactor and alphafluoro-cinnamic acid (Int2) | |||||||||
Components | Ferulic acid decarboxylase 1 | |||||||||
Keywords | LYASE / (de)carboxylase / UbiD / prFMN binding | |||||||||
Function / homology | Function and homology information 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 | Aspergillus niger (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.13 Å | |||||||||
Authors | Bailey, S.S. / Leys, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To be published Title: Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition Authors: Bailey, S.S. / Payne, K.A.P. / Saaret, A. / Marshall, S.A. / Gostimskaya, I. / Kosov, I. / Fisher, K. / Hay, S. / Leys, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r3g.cif.gz | 236.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r3g.ent.gz | 186.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r3g_validation.pdf.gz | 789.5 KB | Display | wwPDB validaton report |
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Full document | 6r3g_full_validation.pdf.gz | 804.2 KB | Display | |
Data in XML | 6r3g_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 6r3g_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r3g ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r3g | HTTPS FTP |
-Related structure data
Related structure data | 6r2pC 6r2rC 6r2tC 6r2zC 6r30C 6r32C 6r33C 6r34C 6r3fC 6r3iC 6r3jC 6r3lC 6r3nC 6r3oC 4za9S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 56334.961 Da / Num. of mol.: 1 / Mutation: E282Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Gene: fdc1, An03g06590 / Production host: Escherichia coli (E. coli) / References: UniProt: A2QHE5, phenacrylate decarboxylase | ||||
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#2: Chemical | ChemComp-MN / | ||||
#3: Chemical | #4: Chemical | ChemComp-JQQ / [( | #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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 6.5, 20 % W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→64.81 Å / Num. obs: 201927 / % possible obs: 99.8 % / Redundancy: 4.8 % / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 1.13→1.17 Å / Mean I/σ(I) obs: 3.01 / Num. unique obs: 19715 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4ZA9 Resolution: 1.13→64.81 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.677 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→64.81 Å
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Refine LS restraints |
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