[English] 日本語
Yorodumi- PDB-5x1j: Vanillate/3-O-methylgallate O-demethylase, LigM, vanillate comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x1j | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Vanillate/3-O-methylgallate O-demethylase, LigM, vanillate 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
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5x1j.cif.gz | 288 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5x1j.ent.gz | 230.1 KB | Display | PDB format |
PDBx/mmJSON format | 5x1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x1j_validation.pdf.gz | 479 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5x1j_full_validation.pdf.gz | 483.3 KB | Display | |
Data in XML | 5x1j_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 5x1j_validation.cif.gz | 77.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/5x1j ftp://data.pdbj.org/pub/pdb/validation_reports/x1/5x1j | HTTPS FTP |
-Related structure data
Related structure data | 5x1iSC 5x1kC 5x1lC 5x1mC 5x1nC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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) / References: UniProt: G2IQS7 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 0.1M LiCl, 25%(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03329 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03329 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.9 Å / Num. obs: 247644 / % possible obs: 99.1 % / Redundancy: 5.5 % / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 3.7 / % possible all: 98.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5X1I Resolution: 1.9→47.816 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.55 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.816 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|