+Open data
-Basic information
Entry | Database: PDB / ID: 3bbd | ||||||
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Title | M. jannaschii Nep1 complexed with S-adenosyl-homocysteine | ||||||
Components | Ribosome biogenesis protein NEP1-like | ||||||
Keywords | TRANSFERASE / methyltransferase / ribosome biogenesis / S-adenosyl-methionine / S-adenosyl-homocysteine / rRNA processing | ||||||
Function / homology | Function and homology information rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Taylor, A.B. / Meyer, B. / Leal, B.Z. / Kotter, P. / Hart, P.J. / Entian, K.-D. / Wohnert, J. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Authors: Taylor, A.B. / Meyer, B. / Leal, B.Z. / Kotter, P. / Schirf, V. / Demeler, B. / Hart, P.J. / Entian, K.D. / Wohnert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bbd.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bbd.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bbd_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3bbd_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3bbd_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3bbd_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbd ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24453.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: Nep1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57977 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 100 mM BisTris-propane, 6-10% polyethylene glycol 400, 30-48% glycerol and 0-400 mM trimethylamine-N-oxide, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 39501 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 30.57 Å2 / Rsym value: 0.107 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 7501 / Rsym value: 0.565 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→46.856 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 37.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→46.856 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.1853 Å
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