+Open data
-Basic information
Entry | Database: PDB / ID: 3rp1 | ||||||
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Title | Crystal structure of Human LAIR-1 in C2 space group | ||||||
Components | Leukocyte-associated immunoglobulin-like receptor 1 | ||||||
Keywords | IMMUNE SYSTEM / structural genomics / collagen receptor / New York Structural Genomics Research Consortium / NYSGRC / PSI-Biology / Ig-like / collagen-binding | ||||||
Function / homology | Function and homology information immune response-regulating signaling pathway / tertiary granule membrane / specific granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Neutrophil degranulation / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sampathkumar, P. / Ramagopal, U.A. / Yan, Q. / Toro, R. / Nathenson, S. / Bonanno, J. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Human LAIR-1 in C2 space group Authors: Sampathkumar, P. / Ramagopal, U.A. / Yan, Q. / Toro, R. / Nathenson, S. / Bonanno, J. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rp1.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rp1.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rp1_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
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Full document | 3rp1_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 3rp1_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 3rp1_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/3rp1 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/3rp1 | HTTPS FTP |
-Related structure data
Related structure data | 3kgrS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11611.771 Da / Num. of mol.: 4 / Fragment: Extracellular domain (UNP residues 22-123) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD305, LAIR-1, LAIR1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6GTX8 #2: Water | ChemComp-HOH / | |
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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: 2.13 Å3/Da / Density % sol: 42.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM calcium choloride, 28% PEG400, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.081 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.081 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 12005 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 59.1 Å2 / Rsym value: 0.112 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4 / Num. unique all: 1173 / Rsym value: 0.639 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KGR Resolution: 2.6→31.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.562 / SU ML: 0.317 / 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: WITH TLS ADDED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.98 Å2 / Biso mean: 42.1602 Å2 / Biso min: 18.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→31.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.669 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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