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Yorodumi- PDB-1smo: Crystal Structure of Human Triggering Receptor Expressed on Myelo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1smo | ||||||
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Title | Crystal Structure of Human Triggering Receptor Expressed on Myeloid Cells 1 (TREM-1) at 1.47 . | ||||||
Components | triggering receptor expressed on myeloid cells 1TREM1 | ||||||
Keywords | IMMUNE SYSTEM / activating receptors / TREM-1 / innate immune system receptor | ||||||
Function / homology | Function and homology information receptor decoy activity / neutrophil-mediated killing of gram-negative bacterium / humoral immune response / neutrophil chemotaxis / DAP12 interactions / Cell surface interactions at the vascular wall / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / scaffold protein binding ...receptor decoy activity / neutrophil-mediated killing of gram-negative bacterium / humoral immune response / neutrophil chemotaxis / DAP12 interactions / Cell surface interactions at the vascular wall / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / scaffold protein binding / adaptive immune response / intracellular signal transduction / innate immune response / cell surface / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.47 Å | ||||||
Authors | Kelker, M.S. / Foss, T.R. / Peti, W. / Teyton, L. / Kelly, J.W. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of Human Triggering Receptor Expressed on Myeloid Cells 1 (TREM-1) at 1.47A. Authors: Kelker, M.S. / Foss, T.R. / Peti, W. / Teyton, L. / Kelly, J.W. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1smo.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1smo.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 1smo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/1smo ftp://data.pdbj.org/pub/pdb/validation_reports/sm/1smo | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 13756.808 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: trem-1 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 RIL (DE3)codon plus / References: UniProt: Q9NP99 #2: Chemical | ChemComp-TLA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.74 % |
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Crystal grow | Temperature: 277 K / pH: 6.3 Details: PEG 4000, Sodium Tartrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.30 |
-Data collection
Diffraction | Mean temperature: 118 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0000, 0.9795, 0.9797, 0.9537 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2003 Details: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220), A FRONT END, VERTICALLY COLLIMATING PREMIRROR, DOUBLE-CRYSTAL SILICON (111) MONOCHROMATOR WITH A FIXED-HEIGHT EXIT BEAM, TOROIDAL FOCUSING MIRROR | |||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220); SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.47→22.03 Å / Num. obs: 55408 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.057 / Net I/σ(I): 46.3 | |||||||||||||||
Reflection shell | Resolution: 1.47→1.51 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3 / Rsym value: 0.452 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.47→22.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 18.5 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→22.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.47→1.51 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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