+Open data
-Basic information
Entry | Database: PDB / ID: 4uw5 | ||||||
---|---|---|---|---|---|---|---|
Title | Human galectin-7 in complex with a galactose based dendron D2-2. | ||||||
Components | HUMAN GALECTIN-7 | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / DENDRIMERS / MULTIVALENCY / CARBOHYDRATE BINDING | ||||||
Function / homology | Function and homology information Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Ramaswamy, S. / Sleiman, M.H. / Masuyer, G. / Arbez-Gindre, C. / Micha-Screttas, M. / Calogeropoulou, T. / Steele, B.R. / Acharya, K.R. | ||||||
Citation | Journal: FEBS J. / Year: 2015 Title: Structural Basis of Multivalent Galactose-Based Dendrimer Recognition by Human Galectin-7. Authors: Ramaswamy, S. / Haj Sleiman, M. / Masuyer, G. / Arbez-Gindre, C. / Micha-Screttas, M. / Calogeropoulou, T. / Steele, B.R. / Acharya, K.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uw5.cif.gz | 176.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uw5.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 4uw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uw5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4uw5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4uw5_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 4uw5_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uw5 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uw5 | HTTPS FTP |
-Related structure data
Related structure data | 4uw3C 4uw4C 4uw6C 1bkzS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15097.046 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47929 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE |
---|---|
Crystal grow | Details: 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9783 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9783 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→55.69 Å / Num. obs: 54509 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 32.54 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BKZ Resolution: 2.04→55.687 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 36.18 / Stereochemistry target values: ML Details: RESIDUES 1-3 ARE DISORDERED DENSITY MODIFICATION PERFORMED. MTZ FILE POST DENSITY MODIFICATION SUBMITTED.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→55.687 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|