+Open data
-Basic information
Entry | Database: PDB / ID: 3t7z | ||||||
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Title | Structure of Methanocaldococcus jannaschii Nop N-terminal domain | ||||||
Components | Nucleolar protein Nop 56/58Nucleolus | ||||||
Keywords | PROTEIN BINDING / alpha beta fold / RNP assembly and methylation / L7Ae / box C/D RNA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Biswas, S. / Maxwell, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity. Authors: Gagnon, K.T. / Biswas, S. / Zhang, X. / Brown, B.A. / Wollenzien, P. / Mattos, C. / Maxwell, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t7z.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t7z.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/3t7z ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t7z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14157.104 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-119) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0694 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58105 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG 8000, 0.1M Sodium cacodylate, 0.2M Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0, 0.97924 | |||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2010 | |||||||||
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. obs: 12790 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 38.4 | |||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.95 / Rsym value: 0.376 / % possible all: 38.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→35.958 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 25.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.792 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→35.958 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.9052 Å / Origin y: 8.9238 Å / Origin z: -17.5078 Å
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Refinement TLS group | Selection details: chain A |