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Yorodumi- PDB-1f38: X-RAY CRYSTALLOGRAPHIC STRUCTURE OF PRECORRIN 8W DECARBOXYLASE, T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f38 | ||||||
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Title | X-RAY CRYSTALLOGRAPHIC STRUCTURE OF PRECORRIN 8W DECARBOXYLASE, THE PRODUCT OF GENE MT0146 IN THE METHANOBACTERIUM THERMOAUTOTROPHICUM GENOME | ||||||
Components | PRECORRIN-8W DECARBOXYLASE | ||||||
Keywords | LYASE / Decarboxylase / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
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 / MAD / Resolution: 2.4 Å | ||||||
Authors | Keller, J.P. / Smith, P.M. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
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.T. / 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 | 1f38.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f38.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 1f38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f38 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f38 | HTTPS FTP |
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-Related structure data
Related structure data | 1kxzC 1l3bC 1l3cC 1l3iC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a tetramer constructed from chains A -> D. |
-Components
#1: Protein | Mass: 21112.131 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Description: GENOMIC DNA / Gene: MT0146 / Plasmid: PET14A DERIVATIVE / 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop Details: Magnesium Chloride, PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 26K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.06884 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06884 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 54692 / Num. obs: 33548 / % possible obs: 73.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 13.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.4→2.51 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.08 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→100 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: X-PLOR 3.851
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Refinement step | Cycle: LAST / Resolution: 2.4→100 Å
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Refine LS restraints |
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