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Yorodumi- PDB-7yua: Structural Insight into a Metal-Dependent Mutase MtdL Revealing a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yua | ||||||
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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 | ||||||
Components | Transglycosylse | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Metal-Dependent Mutase | ||||||
Function / homology | STELLO-like / Reversibly glycosylated polypeptide family / Reversibly glycosylated polypeptide / metal ion binding / GUANOSINE-5'-DIPHOSPHATE / Transglycosylse Function and homology information | ||||||
Biological species | Marinactinospora thermotolerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chi, C.B. / Ma, M. | ||||||
Funding support | 1items
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Citation | Journal: Acs Catalysis / Year: 2023 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yua.cif.gz | 313 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yua.ent.gz | 251.3 KB | Display | PDB format |
PDBx/mmJSON format | 7yua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yua_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7yua_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7yua_validation.xml.gz | 64.1 KB | Display | |
Data in CIF | 7yua_validation.cif.gz | 88.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/7yua ftp://data.pdbj.org/pub/pdb/validation_reports/yu/7yua | HTTPS FTP |
-Related structure data
Related structure data | 7yv0C 7yu9 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41653.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinactinospora thermotolerans (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: G8HX37 #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: containing 18 % PEG 3350, 0.2 M Potassium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å |
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: 2.5→49.91 Å / Num. obs: 58110 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.5→2.57 Å / Rmerge(I) obs: 0.412 / Num. unique obs: 4540 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YU9 7yu9 Resolution: 2.5→46.919 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.11 / 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: 113.42 Å2 / Biso mean: 39.5876 Å2 / Biso min: 14.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→46.919 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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