+Open data
-Basic information
Entry | Database: PDB / ID: 3smz | ||||||
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Title | Human raver1 RRM1-3 domains (residues 39-320) | ||||||
Components | Ribonucleoprotein PTB-binding 1 | ||||||
Keywords | RNA BINDING PROTEIN / RNA binding / ribonucleoprotein / RNA recognition motif / vinculin / alpha-actinin / nucleus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å | ||||||
Authors | Rangarajan, E.S. / Lee, J.H. / Izard, T. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Apo raver1 structure reveals distinct RRM domain orientations. Authors: Rangarajan, E.S. / Lee, J.H. / Izard, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3smz.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3smz.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 3smz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/3smz ftp://data.pdbj.org/pub/pdb/validation_reports/sm/3smz | HTTPS FTP |
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-Related structure data
Related structure data | 3h2uS 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: 31587.953 Da / Num. of mol.: 1 / Fragment: Tandem RRM domains (UNP residues 39-320) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1978, RAVER1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IY67 | ||
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#2: Chemical | #3: 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: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris-HCl (pH 8.5), 24% PEG 3350, 200 mM Lithium sulfate, Vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008 / Details: mirrors | ||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.99→90.09 Å / Num. all: 21480 / Num. obs: 21054 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 41.87 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 29.4 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 29.44 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H2U, chain B Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.9363 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: used TLS refinement
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Displacement parameters | Biso mean: 57.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.306 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.09 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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