+Open data
-Basic information
Entry | Database: PDB / ID: 1o7s | |||||||||
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Title | High resolution structure of Siglec-7 | |||||||||
Components | SIALIC ACID BINDING IG-LIKE LECTIN 7 | |||||||||
Keywords | CELL ADHESION / SIGLEC / IMMUNOGLOBULIN FOLD / SIALIC ACID BINDING PROTEIN / LECTIN / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information sialic acid binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / carbohydrate binding / cell adhesion / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Alphey, M.S. / Attrill, H. / Crocker, P.R. / Van Aalten, D.M.F. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: High Resolution Structures of Siglec-7 - Insights Into Ligand Specificity in the Siglec Family Authors: Alphey, M.S. / Attrill, H. / Crocker, P.R. / Van Aalten, D.M.F. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o7s.cif.gz | 41.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o7s.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 1o7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/1o7s ftp://data.pdbj.org/pub/pdb/validation_reports/o7/1o7s | HTTPS FTP |
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-Related structure data
Related structure data | 1o7vC 1qfoS C: citing same article (ref.) 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: 14655.292 Da / Num. of mol.: 1 / Fragment: V-SET SIALIC ACID BINDING DOMAIN, RESIDUES 18-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PDEF / Cell line (production host): CHO LEC1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9Y286 |
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#2: Chemical | ChemComp-CYS / |
#3: Sugar | ChemComp-NAG / |
#4: Sugar | ChemComp-NDG / |
#5: 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: 2.026 Å3/Da / Density % sol: 38.145 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M TRI-SODIUM CACODYLATE, PH 6.5, 30 % PEG 8,000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.953758 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953758 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 14144 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 86594 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QFO Resolution: 1.75→30 Å / Rfactor Rfree error: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.564 Å2 / ksol: 0.345425 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |