+Open data
-Basic information
Entry | Database: PDB / ID: 8ouq | |||||||||
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Title | Clr-11 from Rattus norvegicus | |||||||||
Components | C-type lectin domain family 2 member D11 | |||||||||
Keywords | IMMUNE SYSTEM / CTLD FOLD / NATURAL KILLER CELL | |||||||||
Function / homology | Function and homology information natural killer cell lectin-like receptor binding / carbohydrate binding / membrane => GO:0016020 / external side of plasma membrane Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Skalova, T. / Blaha, J. / Kalouskova, B. / Skorepa, O. / Vanek, O. / Dohnalek, J. | |||||||||
Funding support | Czech Republic, European Union, 2items
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Citation | Journal: To Be Published Title: Clr-11 from Rattus norvegicus Authors: Skalova, T. / Blaha, J. / Kalouskova, B. / Skorepa, O. / Vanek, O. / Dohnalek, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ouq.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ouq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ouq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/8ouq ftp://data.pdbj.org/pub/pdb/validation_reports/ou/8ouq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/953 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15729.235 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: STRAIN OF RAT: WAG / Gene: Clec2d11, Clrb, Ocil / Plasmid: PTW5SEC / Cell line (production host): HEK293S GNTI- / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Tissue (production host): HUMAN EMBRYONIC KIDNEY / References: UniProt: Q0H8B9 #2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.11 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2 M sodium formate, 0.1 M sodium acetate, pH 5.0 |
-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: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.23 Å / Num. obs: 34197 / % possible obs: 99.1 % / Redundancy: 13.8 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.032 / Rrim(I) all: 0.12 / Χ2: 0.98 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1687 / CC1/2: 0.967 / Rpim(I) all: 0.258 / Rrim(I) all: 0.968 / Χ2: 0.99 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.23 Å / Cor.coef. Fo:Fc: 0.967 / SU B: 1.993 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.096 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.127 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→46.23 Å
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Refine LS restraints |
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LS refinement shell |
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