+Open data
-Basic information
Entry | Database: PDB / ID: 1dgr | ||||||
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Title | Refined crystal structure of canavalin from jack bean | ||||||
Components | (CANAVALIN) x 3 | ||||||
Keywords | PLANT PROTEIN / DUPLICATED DOMAINS BETA BARREL HELICAL LOOP | ||||||
Function / homology | Function and homology information nutrient reservoir activity / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Canavalia ensiformis (jack bean) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Ko, T.-P. / McPherson, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: X-ray diffraction and atomic force microscopy analysis of twinned crystals: rhombohedral canavalin. Authors: Ko, T.P. / Kuznetsov, Y.G. / Malkin, A.J. / Day, J. / McPherson, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Determination of three crystal structures of canavalin by molecular replacement Authors: Ko, T.-P. / Ng, J.D. / Day, J. / Greenwood, A. / McPherson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dgr.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dgr.ent.gz | 172.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/1dgr ftp://data.pdbj.org/pub/pdb/validation_reports/dg/1dgr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The trimeric assembly contains three identical subunits of chains A,X,Y; B,V,W; and C,N,M. |
-Components
#1: Protein | Mass: 20640.342 Da / Num. of mol.: 3 / Fragment: RESIDUES 46-223 / Source method: isolated from a natural source Details: LEGUME STORAGE PROTEIN; LIMITED DIGESTION BY TRYPSIN Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477 #2: Protein | Mass: 9073.182 Da / Num. of mol.: 3 / Fragment: RESIDUES 246-324 / Source method: isolated from a natural source Details: LEGUME STORAGE PROTEIN; LIMITED DIGESTION BY TRYPSIN Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477 #3: Protein | Mass: 10269.446 Da / Num. of mol.: 3 / Fragment: RESIDUES 331-423 / Source method: isolated from a natural source Details: LEGUME STORAGE PROTEIN; LIMITED DIGESTION BY TRYPSIN Source: (natural) Canavalia ensiformis (jack bean) / Organ: SEED / Tissue: COTYLEDON / References: UniProt: P50477 #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: Dulbeccos phosphate buffered saline, ammonium hydroxide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal grow | *PLUS Details: Koszelak, S., (1995) Biophys. J., 69, 13. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 23, 1989 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→200 Å / Num. all: 42478 / Num. obs: 37938 / % possible obs: 89.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.0548 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.6→2.8 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.1744 / Num. unique all: 7058 / % possible all: 83 |
-Processing
Software |
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Refinement | Resolution: 2.6→200 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Strong NCS restraints were used.
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Refinement step | Cycle: LAST / Resolution: 2.6→200 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / σ(F): 3 / Rfactor obs: 0.181 / Rfactor Rwork: 0.18 / % reflection Rfree: 8 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.23 / Num. reflection obs: 2283 |