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Yorodumi- PDB-5dbg: Crystal Structure of Iridoid Synthase from Cantharanthus roseus i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dbg | ||||||
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Title | Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+ | ||||||
Components | Iridoid synthase | ||||||
Keywords | OXIDOREDUCTASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase / inhibitor | ||||||
Function / homology | Function and homology information (S)-8-oxocitronellyl enol synthase / monoterpenoid biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Catharanthus roseus (Madagascar periwinkle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Liu, W.D. / Hu, Y.M. / Zheng, Y.Y. / Xu, Z.X. / Ko, T.P. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Structures of Iridoid Synthase from Cantharanthus roseus with Bound NAD(+) , NADPH, or NAD(+) /10-Oxogeranial: Reaction Mechanisms Authors: Hu, Y.M. / Liu, W.D. / Malwal, S.R. / Zheng, Y.Y. / Feng, X.X. / Ko, T.P. / Chen, C.C. / Xu, Z.X. / Liu, M.X. / Han, X. / Gao, J. / Oldfield, E. / Guo, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dbg.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dbg.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dbg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5dbg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5dbg_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5dbg_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/5dbg ftp://data.pdbj.org/pub/pdb/validation_reports/db/5dbg | HTTPS FTP |
-Related structure data
Related structure data | 5dbfC 5dbiC 2v6fS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 26 - 390 / Label seq-ID: 1 - 365
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-Components
#1: Protein | Mass: 42283.418 Da / Num. of mol.: 2 / Fragment: UNP residues 26-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle) Plasmid: pET32Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7WDL7, EC: 1.3.1.99 #2: Chemical | #3: 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: 2.31 Å3/Da / Density % sol: 46.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Ammonium Acetate, Sodium Acetate trihydrate, Polyethylene Glycol 4000, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→25 Å / Num. obs: 54153 / % possible obs: 96.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.059 / Rrim(I) all: 0.121 / Χ2: 1.418 / Net I/av σ(I): 15.453 / Net I/σ(I): 9.6 / Num. measured all: 212900 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V6F Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2273 / WRfactor Rwork: 0.1747 / FOM work R set: 0.8223 / SU B: 4.181 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1759 / SU Rfree: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.09 Å2 / Biso mean: 27.46 Å2 / Biso min: 13.79 Å2
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Refinement step | Cycle: final / Resolution: 1.95→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 21902 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.95→1.99 Å
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