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- PDB-7yv0: Structural Insight into a Metal-Dependent Mutase MtdL Revealing a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yv0 | ||||||
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Title | Structural Insight into a Metal-Dependent Mutase MtdL Revealing an Arginine Residue Covalently Mediated Interconversion between Nucleotide-Based furanose and pyranose | ||||||
![]() | Transglycosylse | ||||||
![]() | BIOSYNTHETIC PROTEIN / Metal-Dependent Mutase | ||||||
Function / homology | STELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / Transglycosylse![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chi, C.B. / Ma, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Insight into a Metal-Dependent Mutase Revealing an Arginine Residue-Covalently Mediated Interconversion between Nucleotide-Based Pyranose and Furanose. Authors: Chi, C.B. / Xu, R. / Chen, Q.Q. / Zhang, X.H. / Shi, X.M. / Jin, H.W. / Yin, F. / Jia, H.L. / Zhang, L.R. / Yang, D.H. / Ju, J.H. / Li, Q.L. / Ma, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.9 KB | Display | ![]() |
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PDB format | ![]() | 121.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 465 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yuaC C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41653.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: G8HX37 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 8000, 0.1 M HEPES 7.5 |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→49.14 Å / Num. obs: 37896 / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.34→2.42 Å / Rmerge(I) obs: 0.275 / Num. unique obs: 3686 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 87.85 Å2 / Biso mean: 42.7832 Å2 / Biso min: 22.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.34→31.191 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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