+Open data
-Basic information
Entry | Database: PDB / ID: 1qdc | |||||||||
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Title | MAN(APLHA1-6)MAN(ALPHA1-O)METHYL CONCANAVALIN A COMPLEX | |||||||||
Components | PROTEIN (CONCANAVALIN A) | |||||||||
Keywords | SUGAR BINDING PROTEIN / PLANT LECTIN / CARBOHYDRATE BINDING / DIMANNOSE / CONCANAVALIN A | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Canavalia ensiformis (jack bean) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Bouckaert, J. / Loris, R. / Wyns, L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A. Authors: Bouckaert, J. / Hamelryck, T.W. / Wyns, L. / Loris, R. #1: Journal: J.Biol.Chem. / Year: 1996 Title: Concanavalin a Crystallized in Complex with the Trisaccharide 3,6-Di-O-(Alpha- D-Mannopyranosyl)-Alpha-D-Mannopyranoside Authors: Loris, R. / Maes, D. / Poortmans, F. / Wyns, L. / Bouckaert, J. #2: Journal: J.Biol.Chem. / Year: 1996 Title: Structural Basis of Trimannoside Recognition by Concanavalin A Authors: Naismith, J.H. / Field, R.A. #3: Journal: Biochemistry / Year: 1994 Title: Thermodynamics of Lectin-Carbohydrate Interactions. Titration Microcalorimetry Measurements of the Binding of N-Linked Carbohydrates and Ovalbumin to concanavalin A Authors: Mandal, D.K. / Kishore, N. / Brewer, C.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qdc.cif.gz | 201.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qdc.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qdc_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1qdc_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1qdc_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 1qdc_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qdc ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qdc | HTTPS FTP |
-Related structure data
Related structure data | 1qdoC 1enqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS A TETRAMER, COMPOSED OF IDENTICAL MONOMERS OF 237 AMINO ACIDS. THE FOLLOWING RESIDUES ARE IN WEAK ELECTRON DENSITY: 118 AND 119, 150 AND 151, 161 AND 162. |
-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source Details: CO-CRYSTALS OF CONCANAVALIN A WITH METHYL-6--O-(ALPHA-D-MANNOPYRANOSYL)-ALPHA- D-MANNOPYRANOSIDE Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P55915 #2: Polysaccharide | alpha-D-mannopyranose-(1-6)-methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 395 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: 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: 2.38 Å3/Da / Density % sol: 39.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: DROP: 5 MICROLITER 7 MG/ML CON A + 5 MICROLITER 7% JEFFAMINE M-600, 10 % PEG 8000, 50 MM NH4COOH, 5MM MGCL2, 25 MM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 30, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 71100 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.3 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 498686 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ENQ Resolution: 2→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: X-PLOR / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER, 1991
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.276 / % reflection Rfree: 10 % / Rfactor obs: 0.234 |