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Yorodumi- PDB-6rk5: Inter-dimeric interface controls function and stability of S-meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rk5 | ||||||
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Title | Inter-dimeric interface controls function and stability of S-methionine adenosyltransferase from U. urealiticum | ||||||
Components | Methionine adenosyltransferaseS-Adenosylmethionine synthetase enzyme | ||||||
Keywords | TRANSFERASE / synthetase | ||||||
Function / homology | GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Ureaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Shahar, A. / Zarivach, R. / Bershtein, S. / Kleiner, D. / Shmulevich, F. | ||||||
Funding support | Israel, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: The interdimeric interface controls function and stability of Ureaplasma urealiticum methionine S-adenosyltransferase. Authors: Kleiner, D. / Shmulevich, F. / Zarivach, R. / Shahar, A. / Sharon, M. / Ben-Nissan, G. / Bershtein, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rk5.cif.gz | 559 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rk5.ent.gz | 469.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/6rk5 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/6rk5 | HTTPS FTP |
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-Related structure data
Related structure data | 6rjsSC 6rk7C 6rkaC 6rkcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42880.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ureaplasma urealyticum serovar 7 str. ATCC 27819 (bacteria) Gene: metK, UUR7_0462 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: B2NE58, methionine adenosyltransferase #2: 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: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1M Hepes pH 7.4 and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.6 Å / Num. obs: 42328 / % possible obs: 96.8 % / Redundancy: 7.1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.394 / Num. unique obs: 13239 / CC1/2: 0.717 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RJS Resolution: 2.6→47.6 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.6→47.6 Å
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