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Yorodumi- PDB-3s6e: Crystal structure of a RNA binding motif protein 39 (RBM39) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s6e | ||||||
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Title | Crystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculuS at 0.95 A resolution | ||||||
Components | RNA-binding protein 39 | ||||||
Keywords | RNA BINDING PROTEIN / Ferredoxin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL | ||||||
Function / homology | Function and homology information Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / RAC3 GTPase cycle / RAC2 GTPase cycle / RS domain binding / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle ...Nuclear Envelope Breakdown / Depolymerization of the Nuclear Lamina / RND3 GTPase cycle / Initiation of Nuclear Envelope (NE) Reformation / RAC3 GTPase cycle / RAC2 GTPase cycle / RS domain binding / RHOD GTPase cycle / mRNA Splicing - Major Pathway / RAC1 GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / RHOG GTPase cycle / U1 snRNP binding / regulation of mRNA splicing, via spliceosome / centriolar satellite / RNA splicing / mRNA processing / microtubule cytoskeleton / nuclear speck / protein-containing complex / RNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.95 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a RNA binding motif protein 39 (RBM39) from Mus musculus at 0.95 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s6e.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s6e.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3s6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/3s6e ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s6e | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT 300 OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 12713.939 Da / Num. of mol.: 2 / Fragment: sequence database residues 418-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: BC030493, Caper, Rbm39, Rnpc2 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8VH51 #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
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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: 2.05 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20.00% polyethylene glycol 6000, 0.1M sodium citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97915 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 5, 2011 Details: Vertical focusing mirror; double crystal Si(111) monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 0.95→28.2 Å / Num. all: 131023 / Num. obs: 131023 / % possible obs: 99.4 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.707 Å2 / Rsym value: 0.063 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 0.95→28.2 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 0.453 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.CITRATE (CIT) FROM THE CRYSTALLIZATION SOLUTION AND GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.53 Å2 / Biso mean: 11.9317 Å2 / Biso min: 3.7 Å2
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Refinement step | Cycle: LAST / Resolution: 0.95→28.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
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