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Yorodumi- PDB-8pb4: PsiM in complex with SAH and norbaeocystin, orthorhombic crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pb4 | ||||||
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Title | PsiM in complex with SAH and norbaeocystin, orthorhombic crystal form | ||||||
Components | Psilocybin synthase | ||||||
Keywords | TRANSFERASE / Methyltransferase | ||||||
Function / homology | Function and homology information psilocybin biosynthetic process / 4-hydroxytryptamine 4-phosphate methyltransferase activity / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / nucleus Similarity search - Function | ||||||
Biological species | Psilocybe cubensis (magic mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 Å | ||||||
Authors | Werten, S. / Hudspeth, J. / Rupp, B. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Methyl transfer in psilocybin biosynthesis. Authors: Hudspeth, J. / Rogge, K. / Dorner, S. / Mull, M. / Hoffmeister, D. / Rupp, B. / Werten, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pb4.cif.gz | 229.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pb4.ent.gz | 185.5 KB | Display | PDB format |
PDBx/mmJSON format | 8pb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pb4_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8pb4_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8pb4_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8pb4_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pb4 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pb4 | HTTPS FTP |
-Related structure data
Related structure data | 8pb3C 8pb5C 8pb6C 8pb7C 8pb8C 8qxqC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35889.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiM / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DPA9, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | ChemComp-XP6 / Mass: 256.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O4P / Feature type: SUBJECT OF INVESTIGATION | ||||
#4: Chemical | #5: 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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris/HCl pH 8.5, 20% PEG 8000, 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.6888 Å |
Detector | Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 4, 2023 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6888 Å / Relative weight: 1 |
Reflection | Resolution: 0.91→15.39 Å / Num. obs: 230836 / % possible obs: 99.06 % / Redundancy: 13.4 % / Biso Wilson estimate: 11.02 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08633 / Rpim(I) all: 0.02445 / Rrim(I) all: 0.08979 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 0.91→0.9427 Å / Redundancy: 13.6 % / Rmerge(I) obs: 3.04 / Mean I/σ(I) obs: 0.31 / Num. unique obs: 20907 / CC1/2: 0.383 / CC star: 0.744 / Rpim(I) all: 0.857 / Rrim(I) all: 3.16 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.91→15.39 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.91→15.39 Å
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Refine LS restraints |
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LS refinement shell |
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