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Yorodumi- PDB-4hwn: Crystal structure of the second Ig-C2 domain of human Fc-receptor... -
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-Basic information
Entry | Database: PDB / ID: 4hwn | ||||||
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Title | Crystal structure of the second Ig-C2 domain of human Fc-receptor like A (FCRLA), Isoform 9 [NYSGRC-005836] | ||||||
Components | Fc receptor-like A | ||||||
Keywords | IMMUNE SYSTEM / FCRLA / FCRL / Ig-C2 domain / Ig superfamily / Structural genomics / PSI-biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN | ||||||
Function / homology | Function and homology information plasma membrane => GO:0005886 / transmembrane signaling receptor activity / cell differentiation / cell surface receptor signaling pathway / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.006 Å | ||||||
Authors | Kumar, P.R. / Ahmed, M. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chan, M.K. / Fiser, A. / Garforth, S. / Glenn, A.S. / Hillerich, B. ...Kumar, P.R. / Ahmed, M. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chan, M.K. / Fiser, A. / Garforth, S. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Love, J. / Patel, H. / Rubinstein, R. / Seidel, R. / Stead, M. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN) | ||||||
Citation | Journal: to be published Title: Crystal structure of the second Ig-C2 domain of the human Fc-receptor like A, Isoform 9 [NYSGRC-005836] Authors: Kumar, P.R. / Nathenson, S.G. / 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 | 4hwn.cif.gz | 32.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hwn.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/4hwn ftp://data.pdbj.org/pub/pdb/validation_reports/hw/4hwn | HTTPS FTP |
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-Related structure data
Related structure data | 3rjdS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 11949.231 Da / Num. of mol.: 1 / Fragment: UNP residues 169-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FCRL, FCRL1, FCRLA, FCRLM1, FCRX, FREB, UNQ291/PRO329 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q7L513 |
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#2: 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: 1.71 Å3/Da / Density % sol: 28.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Cacodylate pH 6.5, 0.2M Sodium Chloride, 2M Ammonium Sulfate); Cryoprotection (Reservoir + 2M Lithium Sulfate) ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Sodium Cacodylate pH 6.5, 0.2M Sodium Chloride, 2M Ammonium Sulfate); Cryoprotection (Reservoir + 2M Lithium Sulfate), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 5840 / % possible obs: 99 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.07 / Χ2: 0.958 / Net I/σ(I): 31.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3RJD Resolution: 2.006→36.941 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.23 / σ(F): 1.37 / Phase error: 24.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.55 Å2 / Biso mean: 20.0865 Å2 / Biso min: 5.06 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.006→36.941 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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