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Yorodumi- PDB-3v1x: Crystal structure of 2-methylisoborneol synthase from Streptomyce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v1x | ||||||
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Title | Crystal structure of 2-methylisoborneol synthase from Streptomyces coelicolor A3(2) in complex with Mg2+ and 2-fluorogeranyl diphosphate | ||||||
Components | 2-methylisoborneol synthase | ||||||
Keywords | LYASE / class I terpenoid cyclase fold / DDXXXXD motif / NDXXSXXXE motif / 2-methylisoborneol biosynthesis / Biosynthesis of 2-methylisoborneol | ||||||
Function / homology | Function and homology information 2-methylisoborneol synthase / terpene metabolic process / terpene synthase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å | ||||||
Authors | Koksal, M. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structure of 2-Methylisoborneol Synthase from Streptomyces coelicolor and Implications for the Cyclization of a Noncanonical C-Methylated Monoterpenoid Substrate. Authors: Koksal, M. / Chou, W.K. / 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 | 3v1x.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v1x.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 3v1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3v1x_validation.pdf.gz | 720.2 KB | Display | wwPDB validaton report |
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Full document | 3v1x_full_validation.pdf.gz | 722.4 KB | Display | |
Data in XML | 3v1x_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3v1x_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/3v1x ftp://data.pdbj.org/pub/pdb/validation_reports/v1/3v1x | HTTPS FTP |
-Related structure data
Related structure data | 3v1vSC 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
#1: Protein | Mass: 50144.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SC1A4.08, SCBAC12C8.01, SCO7700 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9F1Y6, Lyases; Carbon-oxygen lyases; Acting on phosphates | ||||
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#2: Chemical | #3: Chemical | ChemComp-0FV / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.8 M Succinic acid pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-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: Jul 11, 2011 |
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: 1.95→50 Å / Num. all: 38813 / Num. obs: 37222 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3531 / Rsym value: 0.849 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V1V Resolution: 1.955→46.381 Å / SU ML: 0.21 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 21.41 / 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: 60.325 Å2 / ksol: 0.395 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.955→46.381 Å
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Refine LS restraints |
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LS refinement shell |
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