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Yorodumi- PDB-1l2q: Crystal Structure of the Methanosarcina barkeri Monomethylamine M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l2q | ||||||
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Title | Crystal Structure of the Methanosarcina barkeri Monomethylamine Methyltransferase (MtmB) | ||||||
Components | monomethylamine methyltransferaseMethylamine-corrinoid protein Co-methyltransferase | ||||||
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: 1.7 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 XPL202A(CONFORMER A) AND ...HETEROGEN THE AUTHORS HAVE INDICATED THAT THE METHYL GROUP IN THE RESIDUE XPL202A(CONFORMER A) AND PYL202A(CONFORMER B) 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 | 1l2q.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l2q.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 1l2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/1l2q ftp://data.pdbj.org/pub/pdb/validation_reports/l2/1l2q | 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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-Components
#1: Protein | Mass: 50308.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri (archaea) / References: UniProt: O30642 |
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#2: Chemical | ChemComp-NH4 / |
#3: 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: 4.88 Å3/Da / Density % sol: 74.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M (NH4)2SO4, 0.1M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Mar 23, 2000 |
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: 1.7→20 Å / Num. all: 105886 / Num. obs: 105886 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.7 / Num. unique all: 105886 / Rsym value: 0.281 / % possible all: 94.8 |
Reflection | *PLUS Num. measured all: 513202 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 94.6 % / Rmerge(I) obs: 0.281 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 483332.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 88.4432 Å2 / ksol: 0.413464 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.16 / Rfactor Rfree: 0.174 / Rfactor Rwork: 0.16 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.215 / Rfactor Rwork: 0.205 / Rfactor obs: 0.205 |