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- PDB-1bwu: MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bwu | ||||||
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Title | MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE | ||||||
![]() | (PROTEIN (AGGLUTININ)) x 4 | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chandra, N.R. / Ramachandraiah, G. / Bachhawat, K. / Dam, T.K. / Surolia, A. / Vijayan, M. | ||||||
![]() | ![]() Title: Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity. Authors: Chandra, N.R. / Ramachandraiah, G. / Bachhawat, K. / Dam, T.K. / Surolia, A. / Vijayan, M. #1: ![]() Title: Crystallization and Preliminary Crystallographic Studies on the Mannose- Specific Lectin from Garlic Authors: Chandra, N.R. / Dam, T.K. / Surolia, A. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1msaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | SUBUNITS, CHAINS A AND D and CHAINS P AND Q, FORM 2 INDEPENDENT HETERO-DIMERS IN THE ASYMMETRIC UNIT |
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Components
-Protein , 4 types, 4 molecules ADPQ
#1: Protein | Mass: 11865.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: Protein | Mass: 12124.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#3: Protein | Mass: 11678.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#4: Protein | Mass: 12010.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Sugars / Non-polymers , 2 types, 151 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Sugar | ChemComp-MAN / ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.6 % | |||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS PH 7.0, 1 WEEK, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 KDetails: Chandra, N.R., (1997) Acta Crystallogr., Sect.D, 53, 787. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: MIRRORS | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection | Resolution: 2.4→9 Å / Num. obs: 22244 / % possible obs: 86.6 % / Redundancy: 2.31 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.7 | |||||||||||||||
Reflection shell |
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Reflection shell | *PLUS % possible obs: 12.2 % |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: SNOWDROP LECTIN (PDB ENTRY 1MSA) Resolution: 2.8→9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 32.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.8 Å / Rfactor Rfree error: 0.099 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.534 / % reflection Rfree: 6 % / Rfactor Rwork: 0.426 |