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Yorodumi- PDB-2xs7: Crystal structure of the RRM domain of mouse Deleted in azoosperm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xs7 | ||||||
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Title | Crystal structure of the RRM domain of mouse Deleted in azoospermia- like in complex with Sycp3 RNA, UUGUUU | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / TRANSLATION REGULATION | ||||||
Function / homology | Function and homology information female meiosis II / positive regulation of meiotic nuclear division / translation activator activity / oocyte maturation / 3'-UTR-mediated mRNA stabilization / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome ...female meiosis II / positive regulation of meiotic nuclear division / translation activator activity / oocyte maturation / 3'-UTR-mediated mRNA stabilization / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome / protein-containing complex / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Jenkins, H.T. / Edwards, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Kinked Beta-Strands Mediate High-Affinity Recognition of Mrna Targets by the Germ-Cell Regulator Dazl Authors: Jenkins, H.T. / Edwards, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xs7.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xs7.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xs7_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
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Full document | 2xs7_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 2xs7_validation.xml.gz | 7 KB | Display | |
Data in CIF | 2xs7_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xs7 ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xs7 | HTTPS FTP |
-Related structure data
Related structure data | 2xs2SC 2xs5C 2xsfC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9797.299 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-117 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET-SUMO-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 PLYSS / References: UniProt: Q64368 |
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#2: RNA chain | Mass: 1831.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | Details: 10 MM MAGNESIUM FORMATE, 25% (W/V) PEG 3350 10 MM ZINC ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 16, 2010 Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→29.82 Å / Num. obs: 16096 / % possible obs: 99.1 % / Observed criterion σ(I): 6 / Redundancy: 6.9 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XS2 Resolution: 1.45→29.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.763 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.073 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.568 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→29.83 Å
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Refine LS restraints |
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