+Open data
-Basic information
Entry | Database: PDB / ID: 1nt2 | ||||||
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Title | CRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / AdeMet / binding motif | ||||||
Function / homology | Function and homology information tRNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / rRNA processing / methylation / RNA binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Aittaleb, M. / Rashid, R. / Chen, Q. / Palmer, J.R. / Daniels, C.J. / Li, H. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure and function of archaeal box C/D sRNP core proteins. Authors: Aittaleb, M. / Rashid, R. / Chen, Q. / Palmer, J.R. / Daniels, C.J. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nt2.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nt2.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1nt2 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1nt2 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | a homodimer of two asu heterodimers is generated by the two-fold along the cell diagonal: 1-Y, 1-X, 1-Z |
-Components
#1: Protein | Mass: 24366.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM4304 / Gene: flpA / Plasmid: pET13b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR21(DE3) / References: UniProt: O28192 |
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#2: Protein | Mass: 30092.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM4304 / Gene: AF2088 / Plasmid: pBR / Production host: Escherichia coli (E. coli) / References: UniProt: O28191 |
#3: Chemical | ChemComp-SAM / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 62.92 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.6 / Details: PEG, pH 8.6, VAPOR DIFFUSION, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.9→50 Å / Num. all: 15869 / Num. obs: 12451 / % possible obs: 78.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 11.7 | |||||||||||||||
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1014 / Rsym value: 0.31 / % possible all: 25.5 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. measured all: 75425 / Rmerge(I) obs: 0.122 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 20.5 % / Rmerge(I) obs: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→31.33 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 244888.64 / Data cutoff high rms absF: 244888.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.5356 Å2 / ksol: 0.33134 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→31.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.316 / Rfactor Rwork: 0.254 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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