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- PDB-6m6p: Structure of Marine bacterial laminarinase mutant E135A in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m6p | ||||||
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Title | Structure of Marine bacterial laminarinase mutant E135A in complex with 1,3-beta-cellotriosyl-glucose | ||||||
![]() | laminarinase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, J. / Xu, Y. / Tanokura, M. / Long, L. / Miyakawa, T. | ||||||
![]() | ![]() Title: Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase. Authors: Yang, J. / Xu, Y. / Miyakawa, T. / Long, L. / Tanokura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 46.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jh5C ![]() 6jhjC ![]() 6jiaC ![]() 4crqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 27776.602 Da / Num. of mol.: 1 / Mutation: E135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Sequence details | This protein is E135A mutant. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM MES (pH7.0), 15% (v/v) ethanol, 28% (m/v) PEG20000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 17, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.21→47.82 Å / Num. obs: 11550 / % possible obs: 95.9 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Net I/σ(I): 10.4 / Num. measured all: 74218 / Scaling rejects: 9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CRQ Resolution: 2.27→43.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.981 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 105.99 Å2 / Biso mean: 33.324 Å2 / Biso min: 21.43 Å2
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Refinement step | Cycle: final / Resolution: 2.27→43.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.271→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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