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Yorodumi- PDB-1nth: Crystal structure of the methanosarcina barkeri monomethylamine m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nth | |||||||||
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Title | Crystal structure of the methanosarcina barkeri monomethylamine methyltransferase (MTMB) | |||||||||
Components | Monomethylamine methyltransferase mtmB1 | |||||||||
Keywords | TRANSFERASE / TIM BARREL | |||||||||
Function / homology | Function and homology information methylamine-corrinoid protein Co-methyltransferase / monomethylamine methyltransferase activity / methanogenesis / methylation Similarity search - Function | |||||||||
Biological species | Methanosarcina barkeri (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 Å | |||||||||
Authors | Hao, B. / Gong, W. / Ferguson, T.K. / James, C.M. / Krzycki, J.A. / Chan, M.K. | |||||||||
Citation | Journal: Science / Year: 2002 Title: A new UAG-encoded residue in the structure of a methanogen methyltransferase Authors: Hao, B. / GONG, W. / FERGUSON, T.K. / JAMES, C.M. / KRZYCKI, J.A. / Chan, M.K. | |||||||||
History |
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Remark 600 | HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE PYL202A COULD BE A METHYL ...HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE PYL202A COULD BE A METHYL (CH3), AMINE (NH2), OR HYDOXYL (OH) GROUP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nth.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nth.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1nth ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1nth | 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 on special symmetry positions |
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Details | The biological assembly is a hexamer |
-Components
#1: Protein | Mass: 50291.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri (archaea) / Strain: MS References: UniProt: O30642, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: 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: 4.29 Å3/Da / Density % sol: 71.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 4.3M NACL, 0.1M HEPES, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2001 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. all: 140499 / Num. obs: 140499 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / Num. unique all: 13348 / Rsym value: 0.51 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.55→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.007
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Xplor file |
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