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Yorodumi- PDB-8k06: Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thali... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k06 | ||||||
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Title | Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- PSU, R5P bound K185A mutant | ||||||
Components | Pseudouridine-5'-phosphate glycosidase | ||||||
Keywords | HYDROLASE / metalloenzyme / glycosylase / C-nucleoside / pseudouridine monophosphate / METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information RNA glycosylase activity / pseudouridylate synthase / pseudouridylate synthase activity / peroxisome / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 Å | ||||||
Authors | Lee, J.Y. / Kim, S.H. / Rhee, S.K. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Rna Biol. / Year: 2024 Title: Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana. Authors: Lee, J. / Kim, S.H. / Rhee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k06.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k06.ent.gz | 152.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k06_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8k06_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 8k06_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 8k06_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/8k06 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/8k06 | HTTPS FTP |
-Related structure data
Related structure data | 8k05C 8k07C 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: 36123.988 Da / Num. of mol.: 3 / Mutation: K185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PUMY, At1g50510, F11F12.14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q84K35, pseudouridylate synthase #2: Chemical | #3: Chemical | #4: Sugar | ChemComp-RP5 / | #5: 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: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M Lithium sulfate, 0.1M MES pH 6, 20% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 29, 2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.845→50 Å / Num. obs: 81648 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.089 / Rrim(I) all: 0.164 / Χ2: 1.667 / Net I/σ(I): 9.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.845→29.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.845→29.922 Å
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Refine LS restraints |
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LS refinement shell |
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