+Open data
-Basic information
Entry | Database: PDB / ID: 1qot | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | lectin UEA-II complexed with fucosyllactose and fucosylgalactose | |||||||||
Components | CHITIN BINDING LECTIN, UEA-II | |||||||||
Keywords | LECTIN / CARBOHYDRATE BINDING / FUCOSYLLCTOSE / FUCOSYLGALACTOSE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | ULEX EUROPAEUS (furze) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Loris, R. / De Greve, H. / Dao-Thi, M.-H. / Messens, J. / Imberty, A. / Wyns, L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structural Basis of Carbohydrate Recognition by Lectin II from Ulex Europaeus, a Protein with a Promiscuous Carbohydrate Binding Site Authors: Loris, R. / De Greve, H. / Dao-Thi, M.-H. / Messens, J. / Imberty, A. / Wyns, L. #1: Journal: Curr.Opin.Struct.Biol. / Year: 1999 Title: Novel Structures of Plant Lectins and Their Complexes with Carbohydrates Authors: Bouckaert, J. / Hamelryck, T.W. / Wyns, L. / Loris, R. / Hamelryck, T.W. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: The Quaternary Structure of Uea-II, the Chitobiose Specific Lectin from Gorse Authors: Dao-Thi, M.-H. / Rizkallah, P. / Wyns, L. / Poortmans, F. / Loris, R. #3: Journal: Biochim.Biophys.Acta / Year: 1998 Title: Legume Lectin Structure Authors: Loris, R. / Hamelryck, T.W. / Bouckaert, J. / Wyns, L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qot.cif.gz | 190.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qot.ent.gz | 152.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qot_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qot_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1qot_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 1qot_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/1qot ftp://data.pdbj.org/pub/pdb/validation_reports/qo/1qot | HTTPS FTP |
-Related structure data
Related structure data | 1dzqC 1qnwC 1qooSC 1qosC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26093.008 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ULEX EUROPAEUS (furze) / Organ: SEED / References: GenBank: AF190633, UniProt: Q9FVF8*PLUS |
---|
-Sugars , 3 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 2 types, 8 molecules
#4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CA / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 45 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Dao-Thi M.H., (1998) Acta Crystallog. sect., D54, 844. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.909 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 22709 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.08 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3→3.14 Å / Redundancy: 5.11 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.23 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 115280 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 98.7 % / Num. unique obs: 2214 / Num. measured obs: 11313 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UEA-II COMPLEXED WITH NAG (1QOO) Resolution: 3→30 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.291 / Rfactor obs: 0.269 |