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Yorodumi- PDB-5dpl: The structure of PKMT2 from Rickettsia typhi in complex with AdoHcy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dpl | ||||||
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Title | The structure of PKMT2 from Rickettsia typhi in complex with AdoHcy | ||||||
Components | protein lysine methyltransferase 2 | ||||||
Keywords | TRANSFERASE / methyltransferase / rossman fold / sam binding protein / methylation | ||||||
Function / homology | Methyltransferase regulatory domain, predicted / Predicted methyltransferase regulatory domain / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / metal ion binding / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase Function and homology information | ||||||
Biological species | Rickettsia typhi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Noinaj, N. / Abeykoon, A. / He, Y. / Yang, D.C. / Buchanan, S.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Insights into Substrate Recognition and Catalysis in Outer Membrane Protein B (OmpB) by Protein-lysine Methyltransferases from Rickettsia. Authors: Abeykoon, A.H. / Noinaj, N. / Choi, B.E. / Wise, L. / He, Y. / Chao, C.C. / Wang, G. / Gucek, M. / Ching, W.M. / Chock, P.B. / Buchanan, S.K. / Yang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dpl.cif.gz | 214.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dpl.ent.gz | 169.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/5dpl ftp://data.pdbj.org/pub/pdb/validation_reports/dp/5dpl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 61402.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia typhi (strain ATCC VR-144 / Wilmington) (bacteria) Strain: ATCC VR-144 / Wilmington / Gene: RT0101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68XQ5 #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.19 M CaCl2, 0.095 M HEPES-NaOH, pH 7.5, 26.6 % polyethylene glycol 400, 5 % v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 23922 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rsym value: 0.14 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.955 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.61 / 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: 3.2→48.955 Å
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Refine LS restraints |
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LS refinement shell |
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