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Yorodumi- PDB-6eva: Structure of E277Q A. niger fdc1 in complex with a phenylpyruvate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eva | ||||||
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Title | Structure of E277Q A. niger fdc1 in complex with a phenylpyruvate derived adduct to the prenylated flavin cofactor | ||||||
Components | Ferulic acid decarboxylase 1 | ||||||
Keywords | LYASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Bailey, S.S. / David, L. / Payne, K.A.P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis. Authors: Bailey, S.S. / Payne, K.A.P. / Fisher, K. / Marshall, S.A. / Cliff, M.J. / Spiess, R. / Parker, D.A. / Rigby, S.E.J. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eva.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eva.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 6eva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eva_validation.pdf.gz | 793.7 KB | Display | wwPDB validaton report |
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Full document | 6eva_full_validation.pdf.gz | 799.9 KB | Display | |
Data in XML | 6eva_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 6eva_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/6eva ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6eva | HTTPS FTP |
-Related structure data
Related structure data | 6ev3C 6ev4C 6ev5C 6ev6C 6ev7C 6ev8C 6ev9C 6evbC 6evcC 6evdC 6eveC 6evfC 4za4S 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
#1: Protein | Mass: 56334.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus niger (mold) / Gene: fdc1, An03g06590 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2QHE5, phenacrylate decarboxylase | ||||
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#2: Chemical | ChemComp-MN / | ||||
#3: Chemical | #4: Chemical | ChemComp-4MJ / | #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: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→53.14 Å / Num. obs: 66447 / % possible obs: 100 % / Redundancy: 5.5 % / Net I/σ(I): 11.51 |
Reflection shell | Resolution: 1.64→1.699 Å / Redundancy: 5.2 % / Num. unique obs: 6541 / Rrim(I) all: 0.778 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZA4 Resolution: 1.64→53.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.638 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / 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: 16.208 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→53.14 Å
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Refine LS restraints |
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