+Open data
-Basic information
Entry | Database: PDB / ID: 5iml | ||||||
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Title | Nanobody targeting human Vsig4 in Spacegroup P212121 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Nanobody / Complement Receptor / Vsig4 CRIg | ||||||
Function / homology | Function and homology information negative regulation of complement activation, alternative pathway / negative regulation of macrophage activation / complement component C3b binding / complement activation, alternative pathway / negative regulation of interleukin-2 production / negative regulation of T cell proliferation / protein-containing complex / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Camelidae (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Wen, Y. | ||||||
Citation | Journal: Immunobiology / Year: 2017 Title: Structural evaluation of a nanobody targeting complement receptor Vsig4 and its cross reactivity Authors: Wen, Y. / Ouyang, Z. / Schoonooghe, S. / Luo, S. / De Baetselier, P. / Lu, W. / Muyldermans, S. / Raes, G. / Zheng, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iml.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iml.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/5iml ftp://data.pdbj.org/pub/pdb/validation_reports/im/5iml | HTTPS FTP |
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-Related 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: 24606.785 Da / Num. of mol.: 1 / Fragment: UNP residues 19-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VSIG4, CRIg, Z39IG, UNQ317/PRO362 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y279 |
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#2: Antibody | Mass: 14599.001 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli) |
#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: 1.5 Å3/Da / Density % sol: 18.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: (1) 1.2M sodium citrate tribasic dehydrate, 0.1M BIS-TRIS propane pH7.0 and (2) 0.17M Ammonium sulfate, 15% Glycerol, 25.5% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.78 Å / Num. obs: 22570 / % possible obs: 99.49 % / Redundancy: 9.8 % / Net I/σ(I): 12.79 |
-Processing
Software |
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Refinement | Resolution: 1.8→47.78 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -13.9195 Å / Origin y: -9.6314 Å / Origin z: 21.8292 Å
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Refinement TLS group | Selection details: all |