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Yorodumi- PDB-5x1l: Vanillate/3-O-methylgallate O-demethylase, LigM, tetrahydrofolate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x1l | ||||||||||||
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Title | Vanillate/3-O-methylgallate O-demethylase, LigM, tetrahydrofolate complex form | ||||||||||||
Components | Vanillate/3-O-methylgallate O-demethylase | ||||||||||||
Keywords | OXIDOREDUCTASE / Lignin / Sphingobium sp. SYK-6 | ||||||||||||
Function / homology | Function and homology information vanillate/3-O-methylgallate O-demethylase / lignin catabolic process / methyltransferase activity / methylation / cytosol Similarity search - Function | ||||||||||||
Biological species | Sphingobium sp. SYK-6 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Harada, A. / Senda, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: FEBS J. / Year: 2017 Title: The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6 Authors: Harada, A. / Kamimura, N. / Takeuchi, K. / Yu, H.Y. / Masai, E. / Senda, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x1l.cif.gz | 284.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x1l.ent.gz | 226.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x1l_validation.pdf.gz | 969.1 KB | Display | wwPDB validaton report |
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Full document | 5x1l_full_validation.pdf.gz | 979.5 KB | Display | |
Data in XML | 5x1l_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 5x1l_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/5x1l ftp://data.pdbj.org/pub/pdb/validation_reports/x1/5x1l | HTTPS FTP |
-Related structure data
Related structure data | 5x1iSC 5x1jC 5x1kC 5x1mC 5x1nC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 52612.145 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligM, SLG_12740 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2IQS7 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.61 Å3/Da / Density % sol: 52.8 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.5, 0.1M LiCl, 30%(w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 7, 2015 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.775 Å / Num. obs: 248994 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→1.9 Å / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X1I Resolution: 1.9→47.775 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.42 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.775 Å
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Refine LS restraints |
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LS refinement shell |
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