+Open data
-Basic information
Entry | Database: PDB / ID: 5wzi | ||||||
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Title | Structure of APUM23-GGAGUUGACGG | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / SIGNALING PROTEIN / HYDROLASE / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | Function and homology information response to sucrose / response to glucose / regulation of translation / nucleolus / RNA binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Bao, H. / Wang, N. / Wang, C. / Jiang, Y. / Wu, J. / Shi, Y. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Structural basis for the specific recognition of 18S rRNA by APUM23. Authors: Bao, H. / Wang, N. / Wang, C. / Jiang, Y. / Liu, J. / Xu, L. / Wu, J. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wzi.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wzi.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wzi ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wzi | HTTPS FTP |
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-Related structure data
Related structure data | 5wzgSC 5wzhC 5wzjC 5wzkC S: Starting model for refinement C: citing same article (ref.) |
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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: 65626.008 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 85-655 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: APUM23, At1g72320, T10D10.21, T9N14.7 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9C552 |
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#2: RNA chain | Mass: 3602.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#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: 3.46 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.15 M DL-Malic acid (pH 7.0), 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→40 Å / Num. obs: 25175 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 43.05 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.043 / Rrim(I) all: 0.15 / Χ2: 0.954 / Net I/σ(I): 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WZG Resolution: 2.75→39.993 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.26 Å2 / Biso mean: 40.2085 Å2 / Biso min: 13.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→39.993 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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