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Yorodumi- PDB-6caf: High Resolution Structure of Concanavalin B from Jack Bean (Canav... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6caf | ||||||
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Title | High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein | ||||||
Components | Concanavalin B | ||||||
Keywords | PLANT PROTEIN / SEED PROTEIN / chitinase-like protein / MES / Jack Bean | ||||||
Function / homology | Function and homology information chitinase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Canavalia ensiformis (jack bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | McPherson, A. | ||||||
Citation | Journal: To be published Title: High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), a Chitinase-like Protein Authors: McPherson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6caf.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6caf.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 6caf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6caf_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 6caf_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 6caf_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6caf_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/6caf ftp://data.pdbj.org/pub/pdb/validation_reports/ca/6caf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36762.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canavalia ensiformis (jack bean) / Production host: Canavalia ensiformis (jack bean) / References: UniProt: P49347 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.67 % / Description: Extremely elongated hexagonal prisms |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2% saturated ammonium sulfate buffered with Na phosphate at pH 6.5. Room temperature, crystallization in about 1 week. Protein dissolved in 5% NaCl and 0.1 M acetic acid. PH range: 5.5 7.0 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Aug 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→101.31 Å / Num. obs: 73116 / % possible obs: 82 % / Redundancy: 51.5 % / CC1/2: 1 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.022 / Rrim(I) all: 0.168 / Rsym value: 0.158 / Net I/av σ(I): 50 / Net I/σ(I): 50.1 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 794 / CC1/2: 0.71 / Rpim(I) all: 0.331 / Rrim(I) all: 0.918 / Rsym value: 0.78 / % possible all: 18.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→69.27 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.836 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.91 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→69.27 Å
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Refine LS restraints |
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