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Yorodumi- PDB-4za8: Crystal structure of A niger Fdc1 in complex with penta-fluorocin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4za8 | |||||||||
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Title | Crystal structure of A niger Fdc1 in complex with penta-fluorocinnamic acid | |||||||||
Components | Putative uncharacterized protein An03g06590 | |||||||||
Keywords | LYASE / (de)carboxylase / prenylated flavin / UbiD-like enzyme | |||||||||
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 / Resolution: 1.06 Å | |||||||||
Authors | Payne, K.A.P. / Leys, D. | |||||||||
Citation | Journal: Nature / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4za8.cif.gz | 242.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4za8.ent.gz | 188.8 KB | Display | PDB format |
PDBx/mmJSON format | 4za8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/4za8 ftp://data.pdbj.org/pub/pdb/validation_reports/za/4za8 | HTTPS FTP |
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-Related structure data
Related structure data | 4za4C 4za5C 4za7C 4za9C 4zaaC 4zabC 4zacC 4zadC 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
-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.) Aspergillus niger (mold) / Gene: An03g06590 / Production host: Escherichia coli (E. coli) References: UniProt: A2QHE5, 4-hydroxybenzoate decarboxylase |
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-Non-polymers , 6 types, 483 molecules
#2: Chemical | ChemComp-4LU / | ||||
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#3: Chemical | ChemComp-FZZ / | ||||
#4: Chemical | ChemComp-MN / | ||||
#5: Chemical | #6: Chemical | ChemComp-F5C / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→64.81 Å / Num. obs: 231449 / % possible obs: 99.96 % / Redundancy: 5.2 % / Rpim(I) all: 0.039 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.06→1.09 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.5 / Rpim(I) all: 0.339 / % possible all: 99.98 |
-Processing
Software |
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Refinement | Resolution: 1.06→64.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.971 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / 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: 10.321 Å2
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Refinement step | Cycle: 1 / Resolution: 1.06→64.81 Å
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Refine LS restraints |
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