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Open data
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Basic information
Entry | Database: PDB / ID: 1wbf | ||||||
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Title | WINGED BEAN LECTIN, SACCHARIDE FREE FORM | ||||||
![]() | PROTEIN (AGGLUTININ) | ||||||
![]() | SUGAR BINDING PROTEIN / LECTIN (AGGLUTININ) / LEGUME LECTIN / PROTEIN CRYSTALLOGRAPHY / BLOOD GROUP SPECIFICITY / SACCHARIDE FREE FORM | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Manoj, N. / Srinivas, V.R. / Suguna, K. | ||||||
![]() | ![]() Title: Structure of basic winged-bean lectin and a comparison with its saccharide-bound form. Authors: Manoj, N. / Srinivas, V.R. / Suguna, K. #1: ![]() Title: Carbohydrate Specificity and Quaternary Association in Basic Winged Bean Lectin: X-Ray Analysis of the Lectin at 2.5 A Resolution Authors: Prabu, M.M. / Sankaranarayanan, R. / Puri, K.D. / Sharma, V. / Surolia, A. / Vijayan, M. / Suguna, K. #2: ![]() Title: Crystallization and Preliminary X-Ray Studies of the Basic Lectin from Winged Bean (Psophocarpus Tetragonolobus) Authors: Sankaranarayanan, R. / Puri, K.D. / Ganesh, V. / Banerjee, R. / 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 | ![]() | 113.4 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 33.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wblS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8291, -0.006, 0.559), Vector: |
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Components
#1: Protein | Mass: 26636.799 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 61.1 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: CRYSTALS WERE GROWN BY BATCH METHOD IN WHICH 25 MICROLITERS OF AN 80 MG/ML PROTEIN SOLUTION IN 0.02M PHOSPHATE BUFFER AT PH 7.0, CONTAINING 0.15M SODIUM CHLORIDE, 0.025 (W/V) SODIUM AZIDE, ...Details: CRYSTALS WERE GROWN BY BATCH METHOD IN WHICH 25 MICROLITERS OF AN 80 MG/ML PROTEIN SOLUTION IN 0.02M PHOSPHATE BUFFER AT PH 7.0, CONTAINING 0.15M SODIUM CHLORIDE, 0.025 (W/V) SODIUM AZIDE, WAS MIXED WITH 45% MPD IN THE SAME BUFFER AT 20 DEGREES CENTIGRADE. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.6 Å / Num. obs: 26671 / % possible obs: 88.7 % / Redundancy: 1.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.8 / % possible all: 80.6 |
Reflection | *PLUS Num. measured all: 38947 |
Reflection shell | *PLUS % possible obs: 80.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WBL Resolution: 2.3→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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