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Yorodumi- PDB-5dcy: Iridoid synthase G150A mutant from Catharanthus roseus - binary c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dcy | ||||||||||||
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Title | Iridoid synthase G150A mutant from Catharanthus roseus - binary complex with NADP+ | ||||||||||||
Components | Iridoid synthase | ||||||||||||
Keywords | OXIDOREDUCTASE / Iridoid synthase / short chain dehydrogenase / NADPH-dependent / Catharanthus roseus | ||||||||||||
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: 1.45 Å | ||||||||||||
Authors | Caputi, L. / Kries, H. / Stevenson, C.E.M. / Kamileen, M.O. / Sherden, N.H. / Geu-Flores, F. / Lawson, D.M. / O'Connor, S.E. | ||||||||||||
Funding support | United Kingdom, Switzerland, 3items
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Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Structural determinants of reductive terpene cyclization in iridoid biosynthesis. Authors: Kries, H. / Caputi, L. / Stevenson, C.E. / Kamileen, M.O. / Sherden, N.H. / Geu-Flores, F. / Lawson, D.M. / O'Connor, S.E. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dcy.cif.gz | 328.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dcy.ent.gz | 266.8 KB | Display | PDB format |
PDBx/mmJSON format | 5dcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dcy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5dcy_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5dcy_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 5dcy_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/5dcy ftp://data.pdbj.org/pub/pdb/validation_reports/dc/5dcy | HTTPS FTP |
-Related structure data
Related structure data | 5dcuSC 5dcwC 5df1C 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 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: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 23 - 388 / Label seq-ID: 3 - 368
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-Components
#1: Protein | Mass: 41438.566 Da / Num. of mol.: 2 / Fragment: residues 23-388 Source method: isolated from a genetically manipulated source Details: The crystallised protein contained residues 23-388 of the wild-type amino acid sequence. The sequence differed from database entry K7WDL7 by an Asp to Asn change at position 87 and by a Gly ...Details: The crystallised protein contained residues 23-388 of the wild-type amino acid sequence. The sequence differed from database entry K7WDL7 by an Asp to Asn change at position 87 and by a Gly to Ala change at position 150. The N-terminus retained two residues from the nickel affinity cleavage site. Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle) Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): soluBl21 / References: UniProt: K7WDL7, EC: 1.3.1.99 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.45→41.89 Å / Num. obs: 134019 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.04 / Net I/σ(I): 11.4 / Num. measured all: 1102473 | |||||||||||||||||||||||||||
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: 5DCU Resolution: 1.45→41.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1769 / WRfactor Rwork: 0.158 / FOM work R set: 0.8432 / SU B: 2.767 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0661 / SU Rfree: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.4 Å2 / Biso mean: 20.9 Å2 / Biso min: 9.95 Å2
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Refinement step | Cycle: final / Resolution: 1.45→41.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 45184 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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