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Open data
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Basic information
Entry | Database: PDB / ID: 7r7o | ||||||||||||
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Title | Structure of methyltransferase domain of Spb1 boudn to SAM | ||||||||||||
![]() | AdoMet-dependent rRNA methyltransferase SPB1 | ||||||||||||
![]() | TRANSFERASE / ribosome biogenesis / methyltransferase / nucleolus | ||||||||||||
Function / homology | S-ADENOSYLMETHIONINE / : ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cruz, V.E. / Sekulski, K. / Peddada, N. / Erzberger, J.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Post-catalytic rRNA binding by the DEAD-box ATPase Spb4 and methyltransferase Spb1 guide the late nucleolar assembly of 60S ribosomes Authors: Cruz, V.E. / Sekulski, K. / Peddada, N. / Sailer, C. / Balasubramanian, S. / Weirich, C.S. / Stengel, F. / Erzberger, J.P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.7 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.6 KB | Display | ![]() |
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Full document | ![]() | 929.4 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6elzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24990.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SPB1, PACBIOSEQ_LOCUS534 / Production host: ![]() ![]() References: UniProt: A0A7I9D0Y8, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20 mM Hepes KOH pH 8 150 mM KCl 0.5 mM TCEP 5% Glycerol 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 66501 / % possible obs: 83.08 % / Redundancy: 8.1 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.037 / Rrim(I) all: 0.109 / Χ2: 0.89 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.58→1.61 Å / Mean I/σ(I) obs: 0.93 / Num. unique obs: 3158 / CC1/2: 0.497 / CC star: 0.815 / Rpim(I) all: 0.037 / Χ2: 0.89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ELZ Resolution: 1.58→42.42 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0965 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→42.42 Å
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Refine LS restraints |
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LS refinement shell |
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