+Open data
-Basic information
Entry | Database: PDB / ID: 1dgl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE | |||||||||
Components | LECTIN | |||||||||
Keywords | LECTIN / SACCHARIDE BINDING / TRIMANNOSIDE | |||||||||
Function / homology | Function and homology information mannose binding / toxin activity / carbohydrate binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Dioclea grandiflora (mucana) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Rozwarski, D.A. / Swami, B.M. / Brewer, C.F. / Sacchettini, J.C. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 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: Journal: J.Biol.Chem. / Year: 1996 Title: Structural Basis of Trimannoside Recognition by Concanavalin A Authors: Naismith, J.H. / Field, R.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dgl.cif.gz | 105.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dgl.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dgl ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dgl | HTTPS FTP |
---|
-Related structure data
Related structure data | 5cnaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.496, 0.864, -0.087), Vector: |
-Components
#1: Protein | Mass: 25572.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TRIMANNOSIDE COMPLEX / Source: (natural) Dioclea grandiflora (mucana) / References: UniProt: P08902 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.85 Å3/Da / Density % sol: 75 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.5 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.338 / Num. reflection obs: 4349 / Rfactor obs: 0.28 |