+Open data
-Basic information
Entry | Database: PDB / ID: 1azd | ||||||
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Title | CONCANAVALIN FROM CANAVALIA BRASILIENSIS | ||||||
Components | CONBR | ||||||
Keywords | LECTIN / LEGUME LECTIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Canavalia brasiliensis (Brazilian jackbean) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å | ||||||
Authors | Sanz-Aparicio, J. / Hermoso, J. / Grangeiro, T.B. / Calvete, J.J. / Cavada, B.S. | ||||||
Citation | Journal: FEBS Lett. / Year: 1997 Title: The crystal structure of Canavalia brasiliensis lectin suggests a correlation between its quaternary conformation and its distinct biological properties from Concanavalin A. Authors: Sanz-Aparicio, J. / Hermoso, J. / Grangeiro, T.B. / Calvete, J.J. / Cavada, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1azd.cif.gz | 191.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1azd.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 1azd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azd ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azd | HTTPS FTP |
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-Related structure data
Related structure data | 2ctvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 25592.428 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ISOLATED FROM PLANT Source: (natural) Canavalia brasiliensis (Brazilian jackbean) References: UniProt: P55915 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MN / #4: 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: 2.1 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 2 MICRO-L CBR (10 MG/ML) 2 MICRO-L (11-15% PEG 6000, 0.1 M MES PH 6, pH 6.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→28.4 Å / Num. obs: 16811 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.97→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.5 / % possible all: 88.5 |
Reflection | *PLUS Num. measured all: 91275 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 2CTV Resolution: 3→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.13 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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