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Open data
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Basic information
Entry | Database: PDB / ID: 7ehu | |||||||||
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Title | Chitin oligosaccharide binding protein | |||||||||
![]() | Chitin oligosaccharide binding protein NagB2 | |||||||||
![]() | SUGAR BINDING PROTEIN / Chitin oligosaccharide binding protein | |||||||||
Function / homology | triacetyl-beta-chitotriose / DI(HYDROXYETHYL)ETHER![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Itoh, T. / Hibi, T. / Kimoto, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of two solute-binding proteins for N,N' -diacetylchitobiose/ N,N',N'' -triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. Authors: Itoh, T. / Yaguchi, M. / Nakaichi, A. / Yoda, M. / Hibi, T. / Kimoto, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.4 KB | Display | ![]() |
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PDB format | ![]() | 205.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.5 KB | Display | ![]() |
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Full document | ![]() | 815.4 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ehoSC ![]() 7ehpC ![]() 7ehqC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 47325.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG3350, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 114172 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 10.9 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 1.2→1.22 Å / Num. unique obs: 5714 / CC1/2: 0.702 / Rpim(I) all: 0.474 / Rrim(I) all: 1.279 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EHO Resolution: 1.2→29.15 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.64 Å2 / Biso mean: 18.9952 Å2 / Biso min: 7.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→29.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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