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Yorodumi- PDB-4tzd: Crystal structure of Canavalia maritima lectin (ConM) complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tzd | ||||||
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Title | Crystal structure of Canavalia maritima lectin (ConM) complexed with interleukin - 1 beta primer | ||||||
Components |
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Keywords | Carbohydrate binding protein/DNA / Carbohydrate binding protein / Carbohydrate binding protein-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Canavalia lineata (plant) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å | ||||||
Authors | Vieira, D.B.H.A. / Delatorre, P. / Rocha, B.A.M. / Teixeira, C.S. / Silva-Filho, J.C. / Lima, E.M. / Nobrega, R.B. / Cavada, B.S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Canavalia maritima lectin (ConM) complexed with interleukin 1 - beta primer Authors: Vieira, D.B.H.A. / Delatorre, P. / Cavada, B.S. / Nobrega, R.B. / Teixeira, C.S. / Silva-Filho, J.C. / Lima, E.M. / Rocha, B.A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tzd.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tzd.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 4tzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tzd_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 4tzd_full_validation.pdf.gz | 503.1 KB | Display | |
Data in XML | 4tzd_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 4tzd_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/4tzd ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tzd | HTTPS FTP |
-Related structure data
Related structure data | |
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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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-Components
#1: Protein | Mass: 25494.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia lineata (plant) / References: UniProt: P81460 #2: DNA chain | | Mass: 573.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interleukin 1 - beta primer / Source: (synth.) Escherichia coli (E. coli) #3: DNA chain | | Mass: 1166.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interleukin 1 - beta primer / Source: (synth.) Escherichia coli (E. coli) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium 7.5, 30% v/v 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→48.06 Å / Num. obs: 9248 / % possible obs: 94.7 % / Redundancy: 2.7 % / Net I/σ(I): 5.7 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.2→39.24 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.826 / SU B: 31.292 / SU ML: 0.546 / Cross valid method: FREE R-VALUE / ESU R Free: 0.651 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.968 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→39.24 Å
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Refine LS restraints |
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