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Yorodumi- PDB-3n0g: Crystal Structure of Isoprene Synthase from Grey Poplar Leaves (P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n0g | |||||||||
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Title | Crystal Structure of Isoprene Synthase from Grey Poplar Leaves (Populus x canescens) in complex with three Mg2+ ions and dimethylallyl-S-thiolodiphosphate | |||||||||
Components | Isoprene synthase | |||||||||
Keywords | LYASE / TERPENE CYCLASE FOLD / HEMITERPENE SYNTHASE / DDXXD MOTIF / NSE/DTE MOTIF / DIMETHYLALLYL-S-THIOLODIPHOSPHATE | |||||||||
Function / homology | Function and homology information isoprene synthase / isoprene synthase activity / hydrocarbon biosynthetic process / diterpenoid biosynthetic process / chloroplast / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Populus tremula x Populus alba (gray poplar) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Koksal, M. / Christianson, D.W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structure of isoprene synthase illuminates the chemical mechanism of teragram atmospheric carbon emission. Authors: Koksal, M. / Zimmer, I. / Schnitzler, J.P. / 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 | 3n0g.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n0g.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 3n0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/3n0g ftp://data.pdbj.org/pub/pdb/validation_reports/n0/3n0g | HTTPS FTP |
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-Related structure data
Related structure data | 3n0fSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64118.008 Da / Num. of mol.: 2 / Mutation: N59D, K308R, C533W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Populus tremula x Populus alba (gray poplar) Tissue: leaves / Gene: ispS / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AR86, isoprene synthase #2: Chemical | #3: Chemical | ChemComp-MG / #4: 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: 3.37 Å3/Da / Density % sol: 63.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis-Tris, 25% polyethylene glycol 3350, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2009 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 43749 / Num. obs: 43749 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.135 / Rsym value: 0.135 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.628 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N0F Resolution: 2.8→46.4 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→46.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å
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