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- PDB-2ogy: Asn199Ala Mutant of the 5-methyltetrahydrofolate corrinoid/iron s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ogy | ||||||
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Title | Asn199Ala Mutant of the 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase complexed with methyltetrahydrofolate to 2.3 Angstrom resolution | ||||||
![]() | 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase | ||||||
![]() | TRANSFERASE / methyltetrahydrofolate-protein complex / corrionoid / vitamin B12 / TIM barrel | ||||||
Function / homology | ![]() 5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / pteridine-containing compound metabolic process / methionine synthase activity / carbon fixation / cobalamin binding / methyltransferase activity / methylation / calcium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Doukov, T.I. / Drennan, C.L. / Hemmi, H. / Ragsdale, S.W. | ||||||
![]() | ![]() Title: Structural and kinetic evidence for an extended hydrogen-bonding network in catalysis of methyl group transfer. Role of an active site asparagine residue in activation of methyl transfer by methyltransferases. Authors: Doukov, T.I. / Hemmi, H. / Drennan, C.L. / Ragsdale, S.W. #1: ![]() Title: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Authors: Doukov, T. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121 KB | Display | ![]() |
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PDB format | ![]() | 92.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 886.4 KB | Display | ![]() |
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Full document | ![]() | 895.4 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e7fC ![]() 1f6yS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28595.096 Da / Num. of mol.: 2 / Mutation: N199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 8-15% PEGMME 5000, 0.05M CALCIUM ACETATE, 20% GLYCEROL, 0.05M HEPES BUFFER; 3-FOLD MOLAR EXCESS OF THE MTHF SUBSTRATE (SCHRICKS LABOLATORIES, JONA, SWITZERLAND). THE SUPERSATURATION OF THE ...Details: 8-15% PEGMME 5000, 0.05M CALCIUM ACETATE, 20% GLYCEROL, 0.05M HEPES BUFFER; 3-FOLD MOLAR EXCESS OF THE MTHF SUBSTRATE (SCHRICKS LABOLATORIES, JONA, SWITZERLAND). THE SUPERSATURATION OF THE PRECIPITANT SOLUTION REQUIRED DILUTION OF THE PROTEIN-CH3-H4FOLATE COMPLEX BY 50-100-FOLD IN ORDER TO OBTAIN SINGLE CRYSTALS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 2002 |
Radiation | Monochromator: SI(111) or SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91938 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.73 Å / Num. obs: 24151 / % possible obs: 99.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1752 / Rsym value: 0.385 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F6Y Resolution: 2.3→40.19 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: REFMAC was also used for the refinement.
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Refinement step | Cycle: LAST / Resolution: 2.3→40.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å
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