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- PDB-4j5o: Room temperature crystal structure of a RNA binding motif protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j5o | ||||||
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Title | Room temperature crystal structure of a RNA binding motif protein 39 (Rbm39) from Mus musculus at 1.11 A resolution | ||||||
![]() | RNA-binding protein 39 | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
![]() | ![]() Title: Room temperature crystal structure of a RNA binding motif protein 39 (Rbm39) from Mus musculus at 1.11 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.2 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3s6eS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12573.253 Da / Num. of mol.: 2 / Fragment: UNP residues 418-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() Sequence details | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.72 % |
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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: 296 K / Ambient temp details: room temperature Crystal support: loop mounted and sealed with a MiTeGen MicroRT polyester capillary | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2012 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.11→28.551 Å / Num. obs: 75696 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 10.629 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3s6e Resolution: 1.11→28.551 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.743 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 57.61 Å2 / Biso mean: 17.5736 Å2 / Biso min: 7.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.11→28.551 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.11→1.139 Å / Total num. of bins used: 20
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