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Yorodumi- PDB-1b2p: NATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b2p | ||||||
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Title | NATIVE MANNOSE-SPECIFIC BULB LECTIN FROM SCILLA CAMPANULATA (BLUEBELL) AT 1.7 ANGSTROMS RESOLUTION | ||||||
Components | PROTEIN (LECTIN) | ||||||
Keywords | SUGAR BINDING PROTEIN / MANNOSE-BINDING LECTIN / MONOCOT / AGLUTININ / BLUEBELL BULBS / PROTEIN- CARBOHYDRATE INTERACTIONS | ||||||
Function / homology | Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta / Lectin SCAman Function and homology information | ||||||
Biological species | Hyacinthoides hispanica (Spanish bluebell) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wood, S.D. / Wright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / Peumans, W.J. / Van Damme, E.J.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of the native (unligated) mannose-specific bulb lectin from Scilla campanulata (bluebell) at 1.7 A resolution. Authors: Wood, S.D. / Wright, L.M. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. / Peumans, W.J. / Van Damme, E.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallisation and Preliminary Structural Studies of Scilla Campanulata Lectin Complexed with Alpha (1-6)-Mannobiose Authors: Wright, L.M. / Wood, S.D. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Scilla Campanulata Agglutinin Crystallized in Complex with the Trimannoside Alpha-D-Man-(1-6)-[Alpha-D-Man-(1-3)]-Alpha-D-Man Authors: Wright, L.M. / Rizkallah, P.J. / Wood, S.D. / Reynolds, C.D. #3: Journal: Protein Pept.Lett. / Year: 1997 Title: Crystallisation and Preliminary Crystallographic Analysis of Scilla Campanulata Lectin Complexed with Alpha-D-Mannose Authors: Wright, L.M. / Wood, S.D. / Reynolds, C.D. / Rizkallah, P.J. / Allen, A.K. #4: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Purification, Crystallisation and Preliminary X-Ray Analysis of a Mannose- Binding Lectin from Bluebell (Scilla Campanulata) Bulbs Authors: Wright, L.M. / Wood, S.D. / Reynolds, C.D. / Rizkallah, P.J. / Peumans, W.J. / Vandamme, E.J.M. / Allen, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b2p.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b2p.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1b2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b2p_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 1b2p_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 1b2p_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1b2p_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b2p ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b2p | HTTPS FTP |
-Related structure data
Related structure data | 1gnaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13209.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: LOCATED IN THE BULBS OF SCILLA CAMPANULATA (BLUEBELL) Source: (natural) Hyacinthoides hispanica (Spanish bluebell) References: UniProt: Q9ZP49 #2: 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: 2.78 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.7 Details: HANGING-DROP VAPOUR-DIFFUSION METHOD WELL: 70% SATURATED AMMONIUM SULPHATE, PH 4.7 DROP: 5.5 MG/ML PROTEIN, 10MM DAP, 600MM PHOSPHATE BUFFERED SALINE, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 13, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 33837 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.039 / Rsym value: 0.1 |
Reflection shell | Highest resolution: 1.7 Å |
Reflection | *PLUS Num. measured all: 161054 |
Reflection shell | *PLUS Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GNA Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.225 / Details: X-PLOR WAS USED INITIALLY
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Displacement parameters | Biso mean: 20.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.186 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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