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Yorodumi- PDB-7nf1: Structure of T. atroviride variant TaFdcV in complex with prFMN-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nf1 | ||||||
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Title | Structure of T. atroviride variant TaFdcV in complex with prFMN-butynoic acid adduct | ||||||
Components | Ferulic acid decarboxylase 1 | ||||||
Keywords | LYASE / decarboxylase / prFMN | ||||||
Function / homology | Function and homology information phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Hypocrea atroviridis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Saaret, A. / Leys, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production. Authors: Saaret, A. / Villiers, B. / Stricher, F. / Anissimova, M. / Cadillon, M. / Spiess, R. / 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 | 7nf1.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nf1.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 7nf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nf1_validation.pdf.gz | 638.5 KB | Display | wwPDB validaton report |
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Full document | 7nf1_full_validation.pdf.gz | 643.2 KB | Display | |
Data in XML | 7nf1_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 7nf1_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/7nf1 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/7nf1 | HTTPS FTP |
-Related structure data
Related structure data | 7neyC 7nf0C 7nf2C 7nf3C 7nf4C 6ev4S 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: 57019.812 Da / Num. of mol.: 2 Mutation: E25N N31G G305A D351R K377H P402V F404Y T405M T429A V445P Q448W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea atroviridis (strain ATCC 20476 / IMI 206040) (fungus) Strain: ATCC 20476 / IMI 206040 / Gene: FDC1, TRIATDRAFT_53567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9NLP8, phenacrylate decarboxylase #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Potassium thiocyanate, sodium bromide, MES, PEG Smear High (BCS screen from Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→64.65 Å / Num. obs: 110826 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.9 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.77→1.8 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5368 / CC1/2: 0.5 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EV4 Resolution: 1.77→64.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.475 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.104 / 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: 22.445 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→64.65 Å
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Refine LS restraints |
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