+Open data
-Basic information
Entry | Database: PDB / ID: 8ci9 | ||||||
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Title | Deoxypodophyllotoxin Synthase in complex with Tris | ||||||
Components | Deoxypodophyllotoxin synthase | ||||||
Keywords | OXIDOREDUCTASE / 2-oxoglutarate / yatein / non heme iron | ||||||
Function / homology | Function and homology information (-)-deoxypodophyllotoxin synthase / phenylpropanoid biosynthetic process / : / 2-oxoglutarate-dependent dioxygenase activity / response to wounding / metal ion binding Similarity search - Function | ||||||
Biological species | Sinopodophyllum hexandrum (Himalayan mayapple) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||
Authors | Ingold, Z. / Lichman, B. / Grogan, G. | ||||||
Funding support | 1items
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Citation | Journal: Front Catal / Year: 2023 Title: Structure and mutation of deoxypodophyllotoxin synthase (DPS) from Podophyllum hexandrum Authors: Ingold, Z. / Grogan, G. / Lichman, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ci9.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ci9.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ci9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/8ci9 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/8ci9 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35311.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinopodophyllum hexandrum (Himalayan mayapple) Gene: 2-ODD, Phex30848 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0N9HQ36, (-)-deoxypodophyllotoxin synthase | ||||
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#2: Chemical | ChemComp-FE / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris; 20% (w/v) PEG MME 2000; pH 6.5 20 mg per mL protein |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→40.13 Å / Num. obs: 56104 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.41→1.43 Å / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2792 / CC1/2: 0.74 / Rpim(I) all: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→40.16 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.062 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 26.267 Å2
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Refinement step | Cycle: 1 / Resolution: 1.41→40.16 Å
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