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- PDB-5bte: Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bte | ||||||
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Title | Crystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+ | ||||||
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![]() | hydrolase/rna / Rai1 / RNA / Decapping / mRNA 5'-processing / hydrolase-rna complex | ||||||
Function / homology | ![]() : / NAD-cap decapping / mRNA 5'-diphosphatase activity / exonuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / RNA binding ...: / NAD-cap decapping / mRNA 5'-diphosphatase activity / exonuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / mRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / RNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, V.Y. / Tong, L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.1 KB | Display | ![]() |
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PDB format | ![]() | 138.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.9 KB | Display | ![]() |
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Full document | ![]() | 495 KB | Display | |
Data in XML | ![]() | 32.3 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 43112.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056 / Gene: AGOS_AFR263C / Production host: ![]() ![]() #2: RNA chain | Mass: 1824.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: AgRai1-pU(S)6-Mn2+ complex was obtained by soaking the free AgRai1 crystal with 10mM pU(s)6 and 10mM MnCl2 overnight in the presence of 20%(w/v) PEG3350 and 10%(v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2014 |
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: 2.4→50 Å / Num. obs: 33896 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.6 / % possible all: 99 |
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Processing
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Refinement | Resolution: 2.4→42.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.542 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.272 / 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: 27.313 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→42.41 Å
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Refine LS restraints |
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