+Open data
-Basic information
Entry | Database: PDB / ID: 5ao5 | ||||||
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Title | Endo180 D1-4, monoclinic form | ||||||
Components | C-TYPE MANNOSE RECEPTOR 2 | ||||||
Keywords | ENDOCYTOSIS / ENDOCYTIC RECEPTOR / FIBRONECTIN TYPE II DOMAIN / C-TYPE LECTIN DOMAIN / COLLAGEN / GELATIN | ||||||
Function / homology | Function and homology information Cross-presentation of soluble exogenous antigens (endosomes) / collagen catabolic process / collagen binding / osteoblast differentiation / endocytosis / signaling receptor activity / carbohydrate binding / focal adhesion / membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Paracuellos, P. / Briggs, D.C. / Carafoli, F. / Loncar, T. / Hohenester, E. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Insights Into Collagen Uptake by C-Type Mannose Receptors from the Crystal Structure of Endo180 Domains 1-4. Authors: Paracuellos, P. / Briggs, D.C. / Carafoli, F. / Loncar, T. / Hohenester, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ao5.cif.gz | 329 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ao5.ent.gz | 269.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ao5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/5ao5 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5ao5 | HTTPS FTP |
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-Related structure data
Related structure data | 5ao6C 1dqgS 1tdqS 3m7pS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54592.484 Da / Num. of mol.: 2 / Fragment: DOMAINS 1-4, RESIDUES 35-511 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCEP-PU / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9UBG0 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | VECTOR-DERIVED APLA AT N-TERMINUS. | |
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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: 3.36 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→62.8 Å / Num. obs: 50153 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 46.16 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.48→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1TDQ, 3M7P, 1DQG Resolution: 2.48→60.158 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→60.158 Å
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Refine LS restraints |
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LS refinement shell |
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