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- PDB-7zop: Carbohydrate binding domain CBM92-B from a multi-catalytic glucan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zop | |||||||||
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Title | Carbohydrate binding domain CBM92-B from a multi-catalytic glucanase-chitinase from Chitinophaga pinensis DSM 2588 in complex with sophorose. | |||||||||
![]() | Glycoside hydrolase family 18 | |||||||||
![]() | CARBOHYDRATE / beta-trefoil / carbohydrate binding domain / beta-glycan | |||||||||
Function / homology | ![]() chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mazurkewich, S. / McKee, L.S. / Lu, Z. / Branden, G. / Larsbrink, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to beta-glucans. Authors: Hao, M.S. / Mazurkewich, S. / Li, H. / Kvammen, A. / Saha, S. / Koskela, S. / Inman, A.R. / Nakajima, M. / Tanaka, N. / Nakai, H. / Branden, G. / Bulone, V. / Larsbrink, J. / McKee, L.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 | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 47.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 854.9 KB | Display | ![]() |
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Full document | ![]() | 856.3 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zohSC ![]() 7zoiC ![]() 7zonC ![]() 7zooC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 16176.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Succinimide substitution observed at Asp Source: (gene. exp.) ![]() Gene: Cpin_2580 / Production host: ![]() ![]() #2: Sugar | ChemComp-BGC / | #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: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 with 25 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976259 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→43.99 Å / Num. obs: 18228 / % possible obs: 87.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.68→1.86 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 911 / CC1/2: 0.473 / % possible all: 47.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ZOH Resolution: 1.68→43.99 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.3902 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 29.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→43.99 Å
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Refine LS restraints |
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LS refinement shell |
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