+Open data
-Basic information
Entry | Database: PDB / ID: 5uba | ||||||
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Title | Human RNA Pseudouridylate Synthase Domain Containing 4 | ||||||
Components | RNA pseudouridylate synthase domain-containing protein 4 | ||||||
Keywords | RNA BINDING PROTEIN / CARM1 / methyltransferase / TP-064 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Isomerases; Intramolecular transferases; Transferring other groups / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / positive regulation of mitochondrial translation / tRNA processing / mitochondrial matrix / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å | ||||||
Authors | DONG, A. / ZENG, H. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: The Crystal Structure of Human Pseudouridylate Synthase Domain Containing 4. To be published Authors: ZENG, H. / DONG, A. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uba.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uba.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 5uba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uba_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 5uba_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | 5uba_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 5uba_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5uba ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5uba | HTTPS FTP |
-Related structure data
Related structure data | 1xpiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33473.094 Da / Num. of mol.: 1 / Fragment: UNP residues 89-365 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPUSD4 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL / References: UniProt: Q96CM3 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-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: 46.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97891 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→50 Å / Num. obs: 44925 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 6.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XPI Resolution: 1.54→38.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.497 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.076 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.66 Å2 / Biso mean: 23.3 Å2 / Biso min: 11.96 Å2
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Refinement step | Cycle: final / Resolution: 1.54→38.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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