+Open data
-Basic information
Entry | Database: PDB / ID: 3m9z | ||||||
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Title | Crystal Structure of extracellular domain of mouse NKR-P1A | ||||||
Components | Killer cell lectin-like receptor subfamily B member 1A | ||||||
Keywords | SIGNALING PROTEIN / C-type lectin-like domain / domain swapping / disulfide bond / receptor / transmembrane protein / natural killer cell receptor | ||||||
Function / homology | Function and homology information regulation of natural killer cell mediated cytotoxicity / signaling receptor activity / carbohydrate binding / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kolenko, P. / Rozbesky, D. / Bezouska, K. / Hasek, J. / Dohnalek, J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Molecular architecture of mouse activating NKR-P1 receptors. Authors: Kolenko, P. / Rozbesky, D. / Vanek, O. / Kopecky, V. / Hofbauerova, K. / Novak, P. / Pompach, P. / Hasek, J. / Skalova, T. / Bezouska, K. / Dohnalek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m9z.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m9z.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 3m9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m9z_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 3m9z_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 3m9z_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3m9z_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/3m9z ftp://data.pdbj.org/pub/pdb/validation_reports/m9/3m9z | HTTPS FTP |
-Related structure data
Related structure data | 1e87S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16008.773 Da / Num. of mol.: 1 Fragment: C-TYPE LECTIN-LIKE EXTRACELLULAR DOMAIN (UNP residues 89 to 227) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Klrb1a, Ly55, Ly55a, Nkrp1a / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3) RIL / References: UniProt: P27811 |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.3M Ammonium phosphate, not buffered, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2009 / Details: MIRRORS, Microdiffractometer MD2 |
Radiation | Monochromator: Si 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. obs: 16416 / % possible obs: 99.7 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999 / Redundancy: 7.4 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2319 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E87 Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 1.995 / SU ML: 0.065 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / Stereochemistry target values: CCP4 STEREOCHEMICAL LIBRARY Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; MAXIMUM LIKELIHOOD REFINEMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.297 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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