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- PDB-7r1l: Clostridium thermocellum CtCBM50 structure in complex with beta-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r1l | ||||||
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Title | Clostridium thermocellum CtCBM50 structure in complex with beta-1,4-GlcNAc trisaccharide | ||||||
![]() | Spore coat assembly protein SafA | ||||||
![]() | SUGAR BINDING PROTEIN / CBM50 / ![]() ![]() | ||||||
Function / homology | ![]() Spore coat assembly protein SafA / CAP domain, YkwD-like / CAP domain / ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ribeiro, D.O. / Costa, R. / Palma, A.S. / Carvalho, A.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Unravelling Clostridium thermocellum LysM domains: a molecular view on the cooperative recognition of chitin and peptidoglycan Authors: Ribeiro, D.O. / Palma, A.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 | ![]() | 46.1 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5k2lS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 6474.537 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #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-ACT / | ![]() #4: 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: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M sodium acetate buffer pH 4.6, 2 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jul 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→49.34 Å / Num. obs: 30139 / % possible obs: 97.1 % / Redundancy: 8.6 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.025 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.735 / Num. unique obs: 1427 / CC1/2: 0.81 / Rpim(I) all: 0.468 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5K2L Resolution: 1.45→49.34 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.035 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 85.44 Å2 / Biso mean: 23.344 Å2 / Biso min: 12.4 Å2
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Refinement step | Cycle: final / Resolution: 1.45→49.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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