+Open data
-Basic information
Entry | Database: PDB / ID: 3zxf | ||||||
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Title | High resolution structure of Human Galectin-7 | ||||||
Components | GALECTIN-7 | ||||||
Keywords | SUGAR BINDING PROTEIN | ||||||
Function / homology | Function and homology information 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: 1.38 Å | ||||||
Authors | Masuyer, G. / Oberg, C.T. / Leffler, H. / Nilsson, U.J. / Acharya, K.R. | ||||||
Citation | Journal: FEBS J. / Year: 2012 Title: Inhibition Mechanism of Human Galectin-7 by a Novel Galactose-Benzylphosphate Inhibitor. Authors: Masuyer, G. / Jabeen, T. / Oberg, C.T. / Leffler, H. / Nilsson, U.J. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zxf.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zxf.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxf ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxf | HTTPS FTP |
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-Related structure data
Related structure data | 3zxeC 1bkzS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15281.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47929 #2: Chemical | ChemComp-ACT / | #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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Crystal grow | pH: 8.1 Details: 50MM SODIUM PHOSPHATE, 300 MM NACL, 15% PEG3350, 20MM IMIDAZOLE, pH 8.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.972 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 52544 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.38→1.43 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.5 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BKZ Resolution: 1.38→47.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.115 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.175 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→47.94 Å
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Refine LS restraints |
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