+Open data
-Basic information
Entry | Database: PDB / ID: 2hvy | ||||||
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Title | Crystal structure of an H/ACA box RNP from Pyrococcus furiosus | ||||||
Components |
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Keywords | ISOMERASE/BIOSYNTHETIC PROTEIN/RNA / H/ACA RNA / RNP / PSEUDOURIDINE synthase / Guide RNA / ISOMERASE-BIOSYNTHETIC PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA pseudouridine(55) synthase activity / tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / positive regulation of telomerase RNA localization to Cajal body / ribonuclease P activity ...tRNA pseudouridine(55) synthase activity / tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / positive regulation of telomerase RNA localization to Cajal body / ribonuclease P activity / tRNA 5'-leader removal / telomerase RNA binding / snoRNA binding / rRNA processing / ribosome biogenesis / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ye, K. | ||||||
Citation | Journal: Nature / Year: 2006 Title: Crystal structure of an H/ACA box ribonucleoprotein particle Authors: Li, L. / Ye, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hvy.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hvy.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hvy_validation.pdf.gz | 896.1 KB | Display | wwPDB validaton report |
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Full document | 2hvy_full_validation.pdf.gz | 902.4 KB | Display | |
Data in XML | 2hvy_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 2hvy_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/2hvy ftp://data.pdbj.org/pub/pdb/validation_reports/hv/2hvy | HTTPS FTP |
-Related structure data
Related structure data | 2ey4S 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
-RNA chain , 1 types, 1 molecules E
#1: RNA chain | Mass: 21021.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Derived from Afu-46 RNA |
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-Protein , 4 types, 4 molecules ABCD
#2: Protein | Mass: 39453.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: truB / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups |
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#3: Protein | Mass: 12340.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: GAR1 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 / References: UniProt: Q8U029 |
#4: Protein | Mass: 7214.603 Da / Num. of mol.: 1 / Mutation: R2K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: NOP10 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 / References: UniProt: Q8U1R4 |
#5: Protein | Mass: 14314.623 Da / Num. of mol.: 1 / Mutation: M2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 / References: UniProt: Q8U160 |
-Non-polymers , 3 types, 120 molecules
#6: Chemical | ChemComp-ATP / |
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#7: Chemical | ChemComp-ZN / |
#8: 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: 2.28 Å3/Da / Density % sol: 46.09 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30% MPD, 35mM CH3COOMg, 10mM ATP, 50mM cacodylate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2006 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 39340 / Num. obs: 39234 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 38 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1950 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EY4 Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 16.054 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.26 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.191 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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