[English] 日本語
Yorodumi- PDB-2vxj: CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vxj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC AT 1.9 A RESOLUTION | |||||||||
Components | PA-I GALACTOPHILIC LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / GLOBOSIDE | |||||||||
Function / homology | Function and homology information heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Blanchard, B. / Nurisso, A. / Hollville, E. / Tetaud, C. / Wiels, J. / Pokorna, M. / Wimmerova, M. / Varrot, A. / Imberty, A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural Basis of the Preferential Binding for Globo-Series Glycosphingolipids Displayed by Pseudomonas Aeruginosa Lectin I. Authors: Blanchard, B. / Nurisso, A. / Hollville, E. / Tetaud, C. / Wiels, J. / Pokorna, M. / Wimmerova, M. / Varrot, A. / Imberty, A. | |||||||||
History |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vxj.cif.gz | 619 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vxj.ent.gz | 514.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vxj ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vxj | HTTPS FTP |
---|
-Related structure data
Related structure data | 1l7lS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
-Components
-Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 24 / Fragment: RESIDUES 2-122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097 |
---|
-Sugars , 4 types, 25 molecules
#2: Polysaccharide | alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-BGC / | |
---|
-Non-polymers , 3 types, 3090 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | N-TERMINAL METHIONINE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE |
---|---|
Crystal grow | pH: 4.6 / Details: 10% PEG 5000 MME, 0.025M KSCN, 0.1M NAAC PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 30, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→55.22 Å / Num. obs: 230909 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.26 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.45 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.08 / % possible all: 89.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L7L Resolution: 1.9→55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.886 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.18 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|