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Yorodumi- PDB-2ek1: Crystal structure of RNA-binding motif of human rna-binding protein 12 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ek1 | ||||||
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Title | Crystal structure of RNA-binding motif of human rna-binding protein 12 | ||||||
Components | RNA-binding protein 12 | ||||||
Keywords | RNA BINDING PROTEIN / RNA recognition motif / dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of RNA splicing / ribonucleoprotein complex / RNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Ihsanawati / Bessho, Y. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of RNA-binding motif of human rna-binding protein 12 Authors: Ihsanawati / Bessho, Y. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ek1.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ek1.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ek1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ek1_validation.pdf.gz | 494.7 KB | Display | wwPDB validaton report |
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Full document | 2ek1_full_validation.pdf.gz | 515.5 KB | Display | |
Data in XML | 2ek1_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 2ek1_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/2ek1 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/2ek1 | HTTPS FTP |
-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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 10067.821 Da / Num. of mol.: 8 / Fragment: residues 861-955 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell Free system / Gene: RBM12, KIAA0765 / Plasmid: PX041122-21 / References: UniProt: Q9NTZ6 #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: 1.91 Å3/Da / Density % sol: 35.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes pH7.5, 25% (w/v) PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97947, 0.97964, 0.964 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006 | ||||||||||||
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. obs: 39769 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.102 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rsym value: 0.312 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→29.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1922580.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.3441 Å2 / ksol: 0.322088 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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