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Yorodumi- PDB-6sxw: Crystal structure of the first RRM domain of human Zinc finger pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sxw | ||||||
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Title | Crystal structure of the first RRM domain of human Zinc finger protein 638 (ZNF638) | ||||||
Components | Zinc finger protein 638 | ||||||
Keywords | TRANSCRIPTION / Zinc finger / RNA binding / RRM | ||||||
Function / homology | Function and homology information RNA splicing / Transcriptional regulation of white adipocyte differentiation / double-stranded DNA binding / nuclear speck / intracellular membrane-bounded organelle / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.751 Å | ||||||
Authors | Newman, J.A. / Aitkenhead, H. / Wang, D. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of the first RRM domain of human Zinc finger protein 638 (ZNF638) Authors: Newman, J.A. / Aitkenhead, H. / Wang, D. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sxw.cif.gz | 28 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sxw.ent.gz | 16.3 KB | Display | PDB format |
PDBx/mmJSON format | 6sxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/6sxw ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sxw | HTTPS FTP |
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-Related structure data
Related structure data | 2cq1S 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: 8443.946 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF638, NP220, ZFML / Production host: Escherichia coli (E. coli) / References: UniProt: Q14966 | ||
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#2: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M tris pH 8.5 -- 2.6M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→18.8 Å / Num. obs: 2464 / % possible obs: 99.7 % / Redundancy: 9.4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.018 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.666 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 343 / CC1/2: 0.724 / Rpim(I) all: 0.569 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | 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: 2CQ1 Resolution: 2.751→18.8 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 209.68 Å2 / Biso mean: 108.5176 Å2 / Biso min: 73.23 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.751→18.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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