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Yorodumi- PDB-8b1v: Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b1v | |||||||||
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Title | Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga | |||||||||
Components | Dihydroprecondylocarpine acetate synthase 2 | |||||||||
Keywords | CYTOSOLIC PROTEIN / Alcohol dehydrogenase | |||||||||
Function / homology | Function and homology information cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / alcohol metabolic process / alcohol dehydrogenase (NADP+) activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Tabernanthe iboga (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.882 Å | |||||||||
Authors | Langley, C. / Basquin, J. / Caputi, L. / O'Connor, S.E. | |||||||||
Funding support | Germany, European Union, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism. Authors: Langley, C. / Tatsis, E. / Hong, B. / Nakamura, Y. / Paetz, C. / Stevenson, C.E.M. / Basquin, J. / Lawson, D.M. / Caputi, L. / O'Connor, S.E. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b1v.cif.gz | 185.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b1v.ent.gz | 118.6 KB | Display | PDB format |
PDBx/mmJSON format | 8b1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/8b1v ftp://data.pdbj.org/pub/pdb/validation_reports/b1/8b1v | HTTPS FTP |
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-Related structure data
Related structure data | 8a3nC 8b25C 8b26C 8b27C 5fi3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.999927984975, -9.47613017704E-5, -0.0120006617997), (-0.00105857201491, 0.996767576052, 0.0803323020716), (0.0119542581796, 0.0803392205036, -0.996695894122)Vector: ...NCS oper: (Code: given Matrix: (-0.999927984975, -9.47613017704E-5, -0.0120006617997), Vector: |
-Components
#1: Protein | Mass: 39280.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tabernanthe iboga (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B8X8Z0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 17% w/v PEG 3350, 200 mM ammonium chloride and 0.75 mM angryline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.882→39.81 Å / Num. obs: 62174 / % possible obs: 99.49 % / Redundancy: 13 % / Biso Wilson estimate: 40.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.05 |
Reflection shell | Resolution: 1.882→1.949 Å / Num. unique obs: 5895 / CC1/2: 0.463 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FI3 Resolution: 1.882→39.81 Å / SU ML: 0.3374 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2973 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.882→39.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.519948193521 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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