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- PDB-7cre: hnRNPK KH3 domain in complex with a ssDNA fragment from the SIRLO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cre | ||||||
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Title | hnRNPK KH3 domain in complex with a ssDNA fragment from the SIRLOIN element | ||||||
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![]() | DNA BINDING PROTEIN/DNA / SRILOIN / hnRNPK / KH3 / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() podosome / RNA processing / spliceosomal complex / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yao, J. / Sun, Q. | ||||||
![]() | ![]() Title: Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN. Authors: Yao, J. / Tu, Y. / Shen, C. / Zhou, Q. / Xiao, H. / Jia, D. / Sun, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.4 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.3 KB | Display | ![]() |
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Full document | ![]() | 438.5 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cruC ![]() 1zziS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 8205.230 Da / Num. of mol.: 1 / Fragment: KH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 4755.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SIRLOIN element / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25 % w/v Polyethylene glycol 3350, 100 mM BIS-TRIS pH 5.5, 200 mM Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 3670 / % possible obs: 98.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.049 / Rrim(I) all: 0.159 / Χ2: 1.003 / Net I/σ(I): 13.7 / Num. measured all: 42330 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZZI Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2938 / WRfactor Rwork: 0.2824 / FOM work R set: 0.5831 / SU B: 95.111 / SU ML: 0.624 / SU Rfree: 0.4102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 457.39 Å2 / Biso mean: 142.491 Å2 / Biso min: 76.14 Å2
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Refinement step | Cycle: final / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.158 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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