+Open data
-Basic information
Entry | Database: PDB / ID: 5bth | ||||||
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Title | Crystal structure of Candida albicans Rai1 | ||||||
Components | Decapping nuclease RAI1 | ||||||
Keywords | HYDROLASE / Rai1 / Decapping / mRNA 5'-processing | ||||||
Function / homology | Function and homology information RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / : / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process ...RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / : / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme regulator activity / mRNA processing / nucleotide binding / RNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Wang, V.Y. / Tong, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes. Authors: Wang, V.Y. / Jiao, X. / Kiledjian, M. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bth.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bth.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 5bth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/5bth ftp://data.pdbj.org/pub/pdb/validation_reports/bt/5bth | HTTPS FTP |
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-Related 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: 45746.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: RAI1, CaO19.13610, CaO19.6230 / Production host: Escherichia coli (E. coli) References: UniProt: Q5AAT0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris and 18% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 23150 / % possible obs: 97 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 6.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Resolution: 2.2→33.09 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.74 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.249 / 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: 55.665 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→33.09 Å
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Refine LS restraints |
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