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Yorodumi- PDB-5ero: Crystal structure of elongation domain of Phomopsis amygdali fusi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ero | ||||||
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Title | Crystal structure of elongation domain of Phomopsis amygdali fusicoccadiene synthase complexed with cobalt ions and pamidronate | ||||||
Components | Fusicoccadiene synthaseFusicocca-2,10(14)-diene synthase | ||||||
Keywords | TRANSFERASE / diterpene synthase / lyase | ||||||
Function / homology | Function and homology information fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Phomopsis amygdali (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Chen, M. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structure and Function of Fusicoccadiene Synthase, a Hexameric Bifunctional Diterpene Synthase. Authors: Chen, M. / Chou, W.K. / Toyomasu, T. / Cane, D.E. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ero.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ero.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ero.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/5ero ftp://data.pdbj.org/pub/pdb/validation_reports/er/5ero | HTTPS FTP |
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-Related structure data
Related structure data | 5er8C 5ermC 5ernC 2q80S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39619.207 Da / Num. of mol.: 3 Fragment: Geranylgeranyl diphosphate synthase, residues 382-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phomopsis amygdali (fungus) / Gene: PaFS / Production host: Escherichia coli (E. coli) References: UniProt: A2PZA5, geranylgeranyl diphosphate synthase #2: Chemical | ChemComp-CO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.01 M cobalt chloride, 0.1 M sodium acetate (pH 4.6), 1.0 M 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 47383 / % possible obs: 99.5 % / Redundancy: 11.3 % / Net I/σ(I): 21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q80 Resolution: 2.55→49.849 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→49.849 Å
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Refine LS restraints |
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LS refinement shell |
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