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Yorodumi- PDB-1l3b: MT0146, THE PRECORRIN-6Y METHYLTRANSFERASE (CBIT) HOMOLOG FROM M.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l3b | ||||||
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Title | MT0146, THE PRECORRIN-6Y METHYLTRANSFERASE (CBIT) HOMOLOG FROM M. THERMOAUTOTROPHICUM, C2 SPACEGROUP W/ LONG CELL | ||||||
Components | Precorrin-6y methyltransferase/putative decarboxylase | ||||||
Keywords | TRANSFERASE / LYASE / STRUCTURAL GENOMICS / BETA BARREL / ROSSMANN FOLD / TETRAMER / METHYLTRANSFERASE / DECARBOXYLASE / STRUCTURE-BASED FUNCTION ASSIGNMENT | ||||||
Function / homology | Function and homology information cobalt-precorrin-6B C5-methyltransferase activity / cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating] / corrin biosynthetic process / protein methyltransferase activity / cobalamin biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMEN / Resolution: 2.65 Å | ||||||
Authors | Keller, J.P. / Smith, P.M. / Benach, J. / Christendat, D. / deTitta, G. / Hunt, J.F. | ||||||
Citation | Journal: Structure / Year: 2002 Title: The Crystal Structure of Mt0146/CbiT Suggests that the Putative Precorrin-8W Decarboxylase is a Methyltransferase Authors: Keller, J.P. / Smith, P.M. / Benach, J. / Christendat, D. / deTitta, G. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l3b.cif.gz | 281.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l3b.ent.gz | 232.9 KB | Display | PDB format |
PDBx/mmJSON format | 1l3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/1l3b ftp://data.pdbj.org/pub/pdb/validation_reports/l3/1l3b | HTTPS FTP |
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-Related structure data
Related structure data | 1f38SC 1kxzC 1l3cC 1l3iC C: citing same article (ref.) S: Starting model for refinement |
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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: 21112.131 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: MTH146 / Plasmid: B834 Codon+ / Production host: Escherichia coli (E. coli) / References: UniProt: O26249 #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: 2.25 Å3/Da / Density % sol: 45.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, MGCL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19-ID / Wavelength: 0.97956 / Wavelength: 0.97956 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2000 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97956 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. all: 91016 / Num. obs: 89924 / % possible obs: 98.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 2.93 % / Rmerge(I) obs: 0.105 |
Reflection shell | Resolution: 2.64→2.69 Å / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.78 / Num. unique all: 4486 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 2.65 Å / Lowest resolution: 40 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.109 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMEN Starting model: PDB ENTRY 1F38 Resolution: 2.65→36.65 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.65→36.65 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å / Rfactor Rfree: 0.2859 / Rfactor Rwork: 0.246 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |