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- PDB-1fay: WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fay | |||||||||
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Title | WINGED BEAN ACIDIC LECTIN COMPLEXED WITH METHYL-ALPHA-D-GALACTOSE (MONOCLINIC FORM) | |||||||||
![]() | ACIDIC LECTIN | |||||||||
![]() | SUGAR BINDING PROTEIN / LEGUME LECTIN / GLYCOSYLATED PROTEIN / H-ANTIGENIC SPECIFICITY / AGGLUTININ | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Manoj, N. / Srinivas, V.R. / Surolia, A. / Vijayan, M. / Suguna, K. | |||||||||
![]() | ![]() Title: Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin. Authors: Manoj, N. / Srinivas, V.R. / Surolia, A. / Vijayan, M. / Suguna, K. #1: ![]() Title: Crystallization and Preliminary Crystallographic Analysis of Winged Bean Acidic Lectin Authors: Manoj, N. / Srinivas, V.R. / Satish, B. / Singha, N.C. / Suguna, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.1 KB | Display | ![]() |
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PDB format | ![]() | 275.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1f9kSC S: Starting model for refinement C: citing same article ( |
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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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4 | ![]()
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Unit cell |
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Details | the biological assembly is a dimer |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 26390.123 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: WINGED BEAN, PSOPHOCARPUS TETRAGONOLOBUS, SEEDS / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 14 molecules ![](data/chem/img/AMG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-AMG / |
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-Non-polymers , 3 types, 96 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Crystals were grown by the hanging-drop method. The drops contained 5 microlitres of 15mg/ml protein, a 20-fold molar excess of methyl-alpha-d-galactose in phosphate buffer pH 7.2 and 2ml of ...Details: Crystals were grown by the hanging-drop method. The drops contained 5 microlitres of 15mg/ml protein, a 20-fold molar excess of methyl-alpha-d-galactose in phosphate buffer pH 7.2 and 2ml of 35%(w/v) PEG 4000. 1ml of 35%(w/v) PEG 4000 was used as the reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Manoj, N., (1999) Acta Crystallogr., D55, 564. | ||||||||||||||||||||||||||||||
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: Oct 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→28 Å / Num. all: 32900 / Num. obs: 69174 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.12 |
Reflection shell | Resolution: 3.3→3.42 Å / Rmerge(I) obs: 0.42 / Num. unique all: 3300 / % possible all: 93.6 |
Reflection | *PLUS Num. obs: 32900 / Num. measured all: 69174 |
Reflection shell | *PLUS % possible obs: 93.6 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: WINGED BEAN ACIDIC LECTIN (PDB CODE 1F9K) Resolution: 3.3→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 162723.17 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.19 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.4 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.32 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.303 |