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Open data
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Basic information
Entry | Database: PDB / ID: 7lv6 | ||||||
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Title | The structure of MalL mutant enzyme S536R from Bacillus subtilis | ||||||
![]() | Oligo-1,6-glucosidase 1 | ||||||
![]() | HYDROLASE / TIM barrel / glycoside hydrolase / enzyme design / Rosetta | ||||||
Function / homology | ![]() oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / oligosaccharide catabolic process / alpha-amylase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hamill, C.J. / Prentice, E.J. / Bahl, C.D. / Truebridge, I.S. / Arcus, V.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Urea binding to guide rational design of mutations that influence enzyme dynamics Authors: Hamill, C.J. / Arcus, V.L. / Prentice, E.J. / Bahl, C. / Truebridge, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 370.2 KB | Display | ![]() |
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PDB format | ![]() | 301.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.6 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m56S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 69305.555 Da / Num. of mol.: 1 / Mutation: S536R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: malL, yvdL, BSU34560 / Plasmid: pPROEX-Htb / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris, pH 8.0, 0.2 M ammonium acetate, 18% w/v PEG10000 |
-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: May 1, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953735 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.1→44.85 Å / Num. obs: 208774 / % possible obs: 94.2 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.112 / Net I/σ(I): 12.7 / Num. measured all: 2270037 / Scaling rejects: 1914 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Resolution: 1.1→1.12 Å
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.36
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4M56 Resolution: 1.1→33.54 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.95 / Stereochemistry target values: ML
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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 max: 69.07 Å2 / Biso mean: 16.1338 Å2 / Biso min: 7.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.1→33.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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