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Yorodumi- PDB-1q8a: Cobalamin-dependent methionine synthase (1-566) from Thermotoga m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q8a | ||||||
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Title | Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+:L-Hcy complex, Se-Met) | ||||||
Components | 5-methyltetrahydrofolate S-homocysteine methyltransferase | ||||||
Keywords | TRANSFERASE / homocysteine / methionine / folate / cobalamin / vitamin b12 | ||||||
Function / homology | Function and homology information methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Evans, J.C. / Huddler, D.P. / Hilgers, M.T. / Romanchuk, G. / Matthews, R.G. / Ludwig, M.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 Title: Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase. Authors: Evans, J.C. / Huddler, D.P. / Hilgers, M.T. / Romanchuk, G. / Matthews, R.G. / Ludwig, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q8a.cif.gz | 228.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8a.ent.gz | 183.9 KB | Display | PDB format |
PDBx/mmJSON format | 1q8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8a ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8a | HTTPS FTP |
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-Related 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: 64102.102 Da / Num. of mol.: 2 / Fragment: MetH_Tm (residues 1-566) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9WYA5, methionine synthase #2: Chemical | #3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.13 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: propylene glycol, glycerol, PEG 8000, citrate, 1,2,3-heptanetriol, cadmium, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003 |
Radiation | 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: 136760 / Num. obs: 125901 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.78 Å / % possible all: 83.7 |
Reflection | *PLUS Highest resolution: 1.65 Å / Num. obs: 147923 / % possible obs: 99.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refinement | *PLUS Highest resolution: 1.65 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.211 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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