+Open data
-Basic information
Entry | Database: PDB / ID: 5sum | ||||||
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Title | Ribosome assembly factor NSA1 | ||||||
Components | Ribosome biogenesis protein NSA1 | ||||||
Keywords | RIBOSOMAL PROTEIN / ribosome assembly / rRNA processing / ATPases associated with diverse cellular activities (AAA) / WD40 domain | ||||||
Function / homology | WDR74/Nsa1 / preribosome, large subunit precursor / ribosomal large subunit biogenesis / rRNA processing / WD40-repeat-containing domain superfamily / nucleolus / nucleus / Ribosome biogenesis protein NSA1 Function and homology information | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Lo, Y.H. / Stanley, R.E. | ||||||
Citation | Journal: To Be Published Title: Ribosome assembly factor Authors: Lo, Y.H. / Stanley, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sum.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sum.ent.gz | 129.1 KB | Display | PDB format |
PDBx/mmJSON format | 5sum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/5sum ftp://data.pdbj.org/pub/pdb/validation_reports/su/5sum | HTTPS FTP |
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-Related structure data
Related structure data | 5suiSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 52385.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NSA1, YGL111W, G2990 / Production host: Escherichia coli (E. coli) / References: UniProt: P53136 #2: 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: 3.45 Å3/Da / Density % sol: 64.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Sodium citrate tribasic / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35831 / % possible obs: 99.8 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 28.96 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 5.58 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5SUI Resolution: 2.8→24.31 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 12.084 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.517 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200 Å2 / Biso mean: 48.085 Å2 / Biso min: 19.93 Å2
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Refinement step | Cycle: final / Resolution: 2.8→24.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.801→2.873 Å / Total num. of bins used: 20
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