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Open data
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Basic information
Entry | Database: PDB / ID: 4qkh | ||||||
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Title | Dimeric form of human LLT1, a ligand for NKR-P1 | ||||||
![]() | C-type lectin domain family 2 member D | ||||||
![]() | IMMUNE SYSTEM / C-type lectin like fold / ligand for human receptor NKR-P1 / glycosylation / deglycosylated after the first GlcNac unit / anchored in membrane on cell surface | ||||||
Function / homology | ![]() transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / endoplasmic reticulum / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Skalova, T. / Blaha, J. / Harlos, K. / Duskova, J. / Koval, T. / Stransky, J. / Hasek, J. / Vanek, O. / Dohnalek, J. | ||||||
![]() | ![]() Title: Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states Authors: Skalova, T. / Blaha, J. / Harlos, K. / Duskova, J. / Koval, T. / Stransky, J. / Hasek, J. / Vanek, O. / Dohnalek, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.7 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.3 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qkgC ![]() 4qkiC ![]() 4qkjC ![]() 3hupS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15692.363 Da / Num. of mol.: 2 / Fragment: extracellular part, UNP residues 72-191 / Mutation: H176C Source method: isolated from a genetically manipulated source Details: protein secreted into medium / Source: (gene. exp.) ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.17 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30%(w/v) polyethylene glycol 6000, 0.1M HEPES, pH 7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2012 / Details: Kirkpatrick Baez mirror pair |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.3 Å / Num. all: 21104 / Num. obs: 21104 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 8.3 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3 / Num. unique all: 1087 / % possible all: 81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HUP Resolution: 1.8→47.3 Å / Cor.coef. Fo:Fc: 0.955 / SU B: 2.024 / SU ML: 0.065 / Cross valid method: throughout (except for the last cycle) / σ(F): 0 / ESU R: 0.148 Stereochemistry target values: CCP4 STEREOCHEMISTRY LIBRARY, VERSION 6.4.0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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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 mean: 27.584 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→47.3 Å
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Refine LS restraints |
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