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Open data
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Basic information
Entry | Database: PDB / ID: 7bth | ||||||
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Title | Mevo lectin- Native form-1 | ||||||
![]() | lectin | ||||||
![]() | SUGAR BINDING PROTEIN / beta-prism I fold lectin / Archeal lectin / heptamer / ring shape structure | ||||||
Function / homology | Jacalin-like lectin domain superfamily / Jacalin-type lectin domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and related studies on Mevo lectin from Methanococcus voltae A3: the first thorough characterization of an archeal lectin and its interactions. Authors: Sivaji, N. / Suguna, K. / Surolia, A. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343 KB | Display | ![]() |
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PDB format | ![]() | 278 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.2 KB | Display | ![]() |
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Full document | ![]() | 804.7 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bsbC ![]() 7bsmC ![]() 7bsnC ![]() 7bt8C ![]() 7bt9C ![]() 7btlC ![]() 4znoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15783.812 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-1334 / A3 / Gene: Mvol_0737 / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | Temperature: 296 K / Method: microbatch / pH: 7 Details: 2.0 M ammonium citrate tribasic, 0.1 M bis tris propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→59.7 Å / Num. obs: 41843 / % possible obs: 100 % / Redundancy: 9.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.22 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6030 / CC1/2: 0.85 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZNO Resolution: 2.6→59.687 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.279 / SU B: 44.401 / SU ML: 0.398 / Average fsc free: 0.8214 / Average fsc work: 0.8346 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.343 Details: Hydrogens have been added in their 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: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.909 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→59.687 Å
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Refine LS restraints |
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