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Open data
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Basic information
Entry | Database: PDB / ID: 1dgl | |||||||||
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Title | LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE | |||||||||
![]() | LECTIN | |||||||||
![]() | LECTIN / SACCHARIDE BINDING / TRIMANNOSIDE | |||||||||
Function / homology | ![]() D-mannose binding / toxin activity / carbohydrate binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rozwarski, D.A. / Swami, B.M. / Brewer, C.F. / Sacchettini, J.C. | |||||||||
![]() | ![]() Title: Crystal structure of the lectin from Dioclea grandiflora complexed with core trimannoside of asparagine-linked carbohydrates. Authors: Rozwarski, D.A. / Swami, B.M. / Brewer, C.F. / Sacchettini, J.C. #1: ![]() Title: Structural Basis of Trimannoside Recognition by Concanavalin A Authors: Naismith, J.H. / Field, R.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.9 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cnaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.496, 0.864, -0.087), Vector: |
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Components
#1: Protein | Mass: 25572.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TRIMANNOSIDE COMPLEX / Source: (natural) ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: 4.85 Å3/Da / Density % sol: 75 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→10 Å / Num. obs: 29915 / % possible obs: 74 % / Redundancy: 3.7 % / Rsym value: 0.067 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.21 / % possible all: 23 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. obs: 26679 / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / % possible obs: 70.5 % / Redundancy: 3.4 % / Num. unique obs: 4349 / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5CNA Resolution: 2.4→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 26679 / Rfactor obs: 0.182 / Rfactor Rfree: 0.247 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.338 / Num. reflection obs: 4349 / Rfactor obs: 0.28 |