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- PDB-4h8u: MUTB inactive double mutant D200A-D415N soaked with sucrose and h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h8u | |||||||||
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Title | MUTB inactive double mutant D200A-D415N soaked with sucrose and having as bound ligands sucrose in molecule A and the reaction product trehalulose in molecule B | |||||||||
![]() | Sucrose isomerase | |||||||||
![]() | ISOMERASE / ISOMALTULOSE SYNTHASE LIKE INACTIVE MUTANT / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING | |||||||||
Function / homology | ![]() glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / : / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / amino acid transport / isomerase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lipski, A. / Haser, R. / Aghajari, N. | |||||||||
![]() | ![]() Title: Insights into product binding in sucrose isomerases from crystal structures of MutB from Rhizobium sp. Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Haser, R. / Mattes, R. / Aghajari, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.5 KB | Display | ![]() |
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PDB format | ![]() | 210.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 56.5 KB | Display | |
Data in CIF | ![]() | 88.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h7vC ![]() 4h8hC ![]() 4h8vC ![]() 4ha1C ![]() 2pwhS 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63893.855 Da / Num. of mol.: 2 / Fragment: TREHALULOSE SYNTHASE MUTB, UNP residues 28-584 / Mutation: D200A, D415N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q2PS28, UniProt: M1E1F6*PLUS, EC: 5.4.11.99 |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/TEU.gif)
#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
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#5: Sugar | ChemComp-TEU / |
-Non-polymers , 3 types, 1460 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / | ||
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#4: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.34 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG10000, 0.1M TRIS-HCL , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2010 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.4 Å / Num. all: 88374 / Num. obs: 83253 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 22.19 Å2 / Rsym value: 0.084 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.69 / Num. unique all: 20684 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PWH Resolution: 2→38.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / SU B: 5.163 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.209 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 18 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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