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Yorodumi- PDB-5x1m: Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x1m | ||||||||||||
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Title | Vanillate/3-O-methylgallate O-demethylase, LigM, protocatechuate-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 | 5x1m.cif.gz | 280.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x1m.ent.gz | 222.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/5x1m ftp://data.pdbj.org/pub/pdb/validation_reports/x1/5x1m | HTTPS FTP |
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-Related structure data
Related structure data | 5x1iSC 5x1jC 5x1kC 5x1lC 5x1nC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 3 molecules ABC
#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 |
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-Non-polymers , 5 types, 339 molecules
#2: Chemical | ChemComp-DHB / #3: Chemical | ChemComp-TRS / #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 2.59 Å3/Da / Density % sol: 52.45 % 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, 25%(w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 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→48.32 Å / Num. obs: 257350 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 14.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X1I Resolution: 1.9→47.533 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.48 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→47.533 Å
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Refine LS restraints |
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LS refinement shell |
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