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Open data
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Basic information
Entry | Database: PDB / ID: 8r3d | ||||||
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Title | Crystal structure of Pent only at pH 8.8 | ||||||
![]() | Beta propeller | ||||||
![]() | SUGAR BINDING PROTEIN / Pentamer / beta propeller / mutivalent / synthetic construct | ||||||
Function / homology | Tachylectin 2 / Tachylectin 2 superfamily / Tachylectin / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Beta propeller![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Flood, R.J. / Crowley, P.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Multivalent Calixarene Complexation of a Designed Pentameric Lectin. Authors: Flood, R.J. / Cerofolini, L. / Fragai, M. / Crowley, P.B. #1: ![]() Title: De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints. Authors: Smock, R.G. / Yadid, I. / Dym, O. / Clarke, J. / Tawfik, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.4 KB | Display | ![]() |
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PDB format | ![]() | 47.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457 KB | Display | ![]() |
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Full document | ![]() | 457.1 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r3bC ![]() 8r3cC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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/peptide | Mass: 5327.980 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NDG / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.54 % / Description: Lack defined edges |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 15% PEG 10000 100 mM Tris-HCl pH 8.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→45.81 Å / Num. obs: 25008 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 17.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.045 / Rrim(I) all: 0.112 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1239 / CC1/2: 0.79 / Rpim(I) all: 0.32 / Rrim(I) all: 0.69 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→45.81 Å
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Refine LS restraints |
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LS refinement shell |
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