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Yorodumi- PDB-3lg5: F198A Epi-isozizaene synthase: Complex with Mg, inorganic pyropho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lg5 | ||||||
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Title | F198A Epi-isozizaene synthase: Complex with Mg, inorganic pyrophosphate and benzyl triethyl ammonium cation | ||||||
Components | Epi-isozizaene synthase | ||||||
Keywords | LYASE / terpenoid cyclase / alpha-helical fold / farnesyl diphosphate / metal-binding / magnesium | ||||||
Function / homology | Function and homology information epi-isozizaene synthase / epi-isozizaene synthase activity / terpene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å | ||||||
Authors | Aaron, J.A. / Lin, X. / Cane, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structure of Epi-Isozizaene Synthase from Streptomyces coelicolor A3(2), a Platform for New Terpenoid Cyclization Templates Authors: Aaron, J.A. / Lin, X. / 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 | 3lg5.cif.gz | 98.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lg5.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 3lg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/3lg5 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/3lg5 | HTTPS FTP |
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-Related structure data
Related structure data | 3kb9SC 3kbkC 3lgkC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43540.781 Da / Num. of mol.: 1 / Mutation: F198A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: cyc1, SCO5222, SC7E4.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K499, epi-isozizaene synthase |
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-Non-polymers , 5 types, 473 molecules
#2: Chemical | #3: Chemical | ChemComp-POP / | #4: Chemical | ChemComp-BTM / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.31 % |
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Crystal grow | Temperature: 275 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 275K |
-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 315r / Detector: CCD / Date: Nov 5, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. all: 45918 / Num. obs: 45831 / Redundancy: 3.6 % / Biso Wilson estimate: 14.09 Å2 / Rsym value: 0.062 / Net I/σ(I): 20.55 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 4564 / Rsym value: 0.238 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KB9 Resolution: 1.641→37.606 Å / SU ML: 0.17 / σ(F): 1.34 / 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 / Bsol: 45.551 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.641→37.606 Å
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Refine LS restraints |
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LS refinement shell |
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