+Open data
-Basic information
Entry | Database: PDB / ID: 3bbh | ||||||
---|---|---|---|---|---|---|---|
Title | M. jannaschii Nep1 complexed with Sinefungin | ||||||
Components | Ribosome biogenesis protein NEP1-like | ||||||
Keywords | TRANSFERASE / methyltransferase / ribosome biogenesis / S-adenosyl-methionine / sinefungin / 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 / MOLECULAR REPLACEMENT / Resolution: 2.25 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3bbh.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3bbh.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bbh_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3bbh_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3bbh_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 3bbh_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bbh ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bbh | HTTPS FTP |
-Related structure data
Related structure data | 3bbdSC 3bbeC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24125.578 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.72 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10 Details: 100 mM glycine, 20-24% polyethylene glycol 400, 30% glycerol and 0-200 mM trimethylamine-N-oxide, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.979 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Oct 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 34563 / Num. obs: 34563 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 48.38 Å2 / Rsym value: 0.053 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3359 / Rsym value: 0.468 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3BBD Resolution: 2.25→41.671 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT
| ||||||||||||||||||||
Displacement parameters | Biso mean: 51.598 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→41.671 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.3162 Å
|