[English] 日本語
Yorodumi- PDB-3nvk: Structural basis for substrate placement by an archaeal box C/D r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nvk | ||||||
---|---|---|---|---|---|---|---|
Title | Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/RNA / Nop domain kink turn methyl transferase / ribosome biogenesis spliceosome biogenesis / TRANSFERASE-RNA complex | ||||||
Function / homology | Function and homology information box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / snoRNA binding / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / rRNA processing / methylation ...box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / snoRNA binding / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / rRNA processing / methylation / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.209 Å | ||||||
Authors | Xue, S. / Wang, R. / Li, H. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Authors: Xue, S. / Wang, R. / Yang, F. / Terns, R.M. / Terns, M.P. / Zhang, X. / Maxwell, E.S. / Li, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3nvk.cif.gz | 324.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3nvk.ent.gz | 258.8 KB | Display | PDB format |
PDBx/mmJSON format | 3nvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/3nvk ftp://data.pdbj.org/pub/pdb/validation_reports/nv/3nvk | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
-Protein , 3 types, 6 molecules AFEHIJ
#1: Protein | Mass: 43470.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M1 #2: Protein | Mass: 14243.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160 #3: Protein | Mass: 26760.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: flpA, PF0059 / Production host: Escherichia coli (E. coli) References: UniProt: Q8U4M2, Transferases; Transferring one-carbon groups; Methyltransferases |
---|
-RNA chain , 2 types, 4 molecules KLGS
#4: RNA chain | Mass: 11009.606 Da / Num. of mol.: 2 / Source method: obtained synthetically #5: RNA chain | Mass: 4156.542 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Non-polymers , 1 types, 2 molecules
#6: Chemical |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 67.85 % |
---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 400 mM potassium chloride, 200 mM-1.5 M sodium chloride, 150-250 mM magnesium acetate, 200 mM ammonium acetate, 50 mM HEPES-NaOH., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. all: 45020 / Num. obs: 42641 / % possible obs: 83.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 80.34 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 3.2→50 Å / % possible all: 83.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.209→39.69 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 31.09 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.429 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.209→39.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|