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Yorodumi- PDB-7xcl: Crystal structure of trimethylamine methyltransferase MttB from M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xcl | ||||||
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Title | Crystal structure of trimethylamine methyltransferase MttB from Methanosarcina barkeri at 2.5 A resolution | ||||||
Components | Trimethylamine methyltransferaseTrimethylamine-corrinoid protein Co-methyltransferase | ||||||
Keywords | TRANSFERASE / pyrrolysine / trimethylamine / methyltransferase / corrinoid protein | ||||||
Function / homology | trimethylamine-corrinoid protein Co-methyltransferase / trimethylamine methyltransferase activity / Trimethylamine methyltransferase, Methanosarcina / Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB) / methanogenesis / methylation / Trimethylamine methyltransferase Function and homology information | ||||||
Biological species | Methanosarcina barkeri MS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Li, J. / Chan, M.K. | ||||||
Funding support | Hong Kong, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex. Authors: Li, J. / Kang, P.T. / Jiang, R. / Lee, J.Y. / Soares, J.A. / Krzycki, J.A. / Chan, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xcl.cif.gz | 578.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xcl.ent.gz | 478.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/7xcl ftp://data.pdbj.org/pub/pdb/validation_reports/xc/7xcl | HTTPS FTP |
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-Related structure data
Related structure data | 7xcmC 7xcnC 2qneS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54854.504 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina barkeri MS (archaea) / Gene: MSBRM_0461 / Production host: Methanosarcina acetivorans C2A (archaea) References: UniProt: A0A0E3QRM4, trimethylamine-corrinoid protein Co-methyltransferase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.15 Å3/Da / Density % sol: 70.35 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop Details: 1 ul protein (8 mg/mL MttB in 20 mM potassium phosphate buffer pH 7.4, 500 mM NaCl, 240 mM imidazole, 20% glycerol), 1 ul reservoir (4% MPD, 0.1 M citric acid pH 4.5) solutions |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99984 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→20 Å / Num. obs: 172408 / % possible obs: 93.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Χ2: 1.058 / Net I/σ(I): 7 / Num. measured all: 932353 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QNE Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 54.8941 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.52 Å2 / Biso mean: 47.1297 Å2 / Biso min: 9.33 Å2
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Refinement step | Cycle: final / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Xplor file |
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