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- PDB-5x1k: Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x1k | ||||||||||||
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Title | Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallate complex form | ||||||||||||
![]() | Vanillate/3-O-methylgallate O-demethylase | ||||||||||||
![]() | OXIDOREDUCTASE / Lignin / Sphingobium sp.SYK-6 | ||||||||||||
Function / homology | ![]() vanillate/3-O-methylgallate O-demethylase / lignin catabolic process / methyltransferase activity / methylation / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Harada, A. / Senda, T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 268 KB | Display | ![]() |
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PDB format | ![]() | 211.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5x1iSC ![]() 5x1jC ![]() 5x1lC ![]() 5x1mC ![]() 5x1nC C: citing same article ( 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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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 259 molecules ![](data/chem/img/7WR.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.62 % 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: ![]() ![]() ![]() |
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: 2.15→48.44 Å / Num. obs: 178538 / % possible obs: 99.7 % / Redundancy: 10.5 % / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.15→2.19 Å / Mean I/σ(I) obs: 1.8 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X1I Resolution: 2.15→44.818 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.01 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: 2.15→44.818 Å
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Refine LS restraints |
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LS refinement shell |
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