[English] 日本語
Yorodumi- PDB-2x3t: Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x3t | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crystal soaked with a synthetic glycopeptide | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | SUGAR BINDING PROTEIN/PEPTIDE / SUGAR BINDING PROTEIN-PEPTIDE COMPLEX / CHITIN-BINDING | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | TRITICUM AESTIVUM (bread wheat) SYNTHETIC CONSTRUCT (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.749 Å | ||||||||||||||||||
Authors | Schwefel, D. / Maierhofer, C. / Wittmann, V. / Diederichs, K. / Welte, W. | ||||||||||||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Structural Basis of Multivalent Binding to Wheat Germ Agglutinin. Authors: Schwefel, D. / Maierhofer, C. / Beck, J.G. / Seeberger, S. / Diederichs, K. / Moller, H.M. / Welte, W. / Wittmann, V. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2x3t.cif.gz | 249.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2x3t.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 2x3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x3t_validation.pdf.gz | 3.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2x3t_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 2x3t_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 2x3t_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/2x3t ftp://data.pdbj.org/pub/pdb/validation_reports/x3/2x3t | HTTPS FTP |
-Related structure data
Related structure data | 2uvoC 2x52C 4amlC 7wgaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide / Sugars , 3 types, 17 molecules ABCDEM
#1: Protein | Mass: 17124.080 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: P10968 #2: Protein/peptide | Mass: 886.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: Sugar | ChemComp-GYV / |
---|
-Non-polymers , 3 types, 48 molecules
#4: Chemical | ChemComp-DBB / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | GYV, DBB (RESIDUES 1170-1173 CHAINS A, B, C, D): CANNOT BE ASSIGNED SEPARATE CHAIN IDS FOR THE ...GYV, DBB (RESIDUES 1170-1173 CHAINS A, B, C, D): CANNOT BE ASSIGNED SEPARATE CHAIN IDS FOR THE CYCLIC LIGAND. IN ABSENCE OF BACKBONE DENSITY, IT IS NOT POSSIBLE TO IDENTIFY THEIR SPECIFIC POSITIONS IN THE CYCLIC LIGAND SINCE THEY MIGHT BE ANY OF THE THREE EQUIVALENT |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE |
---|---|
Crystal grow | pH: 4.9 Details: 0.04M KH2PO4, 20% GLYCEROL, 14%-17% PEG 8000, pH 4.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 19531 / % possible obs: 99.5 % / Observed criterion σ(I): 3.45 / Redundancy: 3.8 % / Biso Wilson estimate: 42.32 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.75→2.91 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.45 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7WGA Resolution: 2.749→32.653 Å / SU ML: 0.46 / σ(F): 1.99 / Phase error: 33.35 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.65 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.24 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.749→32.653 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 5.0362 Å / Origin y: 22.9398 Å / Origin z: 22.8769 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |