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- PDB-8wlb: X-ray structure of Enterobacter cloacae allose-binding protein in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wlb | ||||||
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Title | X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-psicose | ||||||
![]() | Allose ABC transporter | ||||||
![]() | SUGAR BINDING PROTEIN / Allose-binding protein | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / outer membrane-bounded periplasmic space / alpha-D-psicopyranose / Allose ABC transporter![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamitori, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Authors: Kamitori, 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 | ![]() | 126 KB | Display | ![]() |
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PDB format | ![]() | 94.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 796.8 KB | Display | ![]() |
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Full document | ![]() | 797.3 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wl5C ![]() 8wl7C ![]() 8wl9C ![]() 1rpjS C: citing same article ( S: Starting model for refinement |
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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 | Mass: 32821.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-WEB / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 20 mM D-psicose, 100 mM sodium citrate tribasic dihydrate, 22% (w/v) polyethylene glycol 1,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→43.29 Å / Num. obs: 32299 / % possible obs: 98.1 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.71→1.75 Å / Num. unique obs: 2172 / CC1/2: 0.911 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RPJ Resolution: 1.71→43.29 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.07 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.116 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.992 Å2
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Refinement step | Cycle: 1 / Resolution: 1.71→43.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.754 Å / Total num. of bins used: 20
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