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Yorodumi- PDB-4uy5: Crystal structure of Histidine-specific methyltransferase EgtD fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uy5 | ||||||
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Title | Crystal structure of Histidine-specific methyltransferase EgtD from Mycobacterium smegmatis | ||||||
Components | HISTIDINE-SPECIFIC METHYLTRANSFERASE EGTD | ||||||
Keywords | TRANSFERASE / S-ADENOSYL-L-METHIONINE / ANTIOXIDANT | ||||||
Function / homology | Function and homology information : / L-histidine Nalpha-methyltransferase / : / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide / protein methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.997 Å | ||||||
Authors | Jeong, J.H. / Kim, Y.G. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2014 Title: Structural Insights Into the Histidine Trimethylation Activity of Egtd from Mycobacterium Smegmatis. Authors: Jeong, J.H. / Cha, H.J. / Ha, S.C. / Rojviriya, C. / Kim, Y.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uy5.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uy5.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uy5_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 4uy5_full_validation.pdf.gz | 448 KB | Display | |
Data in XML | 4uy5_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4uy5_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/4uy5 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/4uy5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36346.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) References: UniProt: A0R5M8, L-histidine Nalpha-methyltransferase |
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#2: Chemical | ChemComp-IMD / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.45 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.1 M IMIDAZOLE PH9.0, 4.2 M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2012 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 28410 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 26.22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 39 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.7 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.997→27.127 Å / SU ML: 0.28 / σ(F): 1.49 / Phase error: 22.75 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.997→27.127 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.6065 Å / Origin y: 7.5433 Å / Origin z: -0.1317 Å
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Refinement TLS group | Selection details: ALL |