[English] 日本語

- PDB-1f6y: MAD CRYSTAL STRUCTURE ANALYSIS OF METHYLTETRAHYDROFOLATE: CORRINO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1f6y | ||||||
---|---|---|---|---|---|---|---|
Title | MAD CRYSTAL STRUCTURE ANALYSIS OF METHYLTETRAHYDROFOLATE: CORRINOID/IRON-SULFUR PROTEIN METHYLTRANSFERASE (METR) | ||||||
![]() | 5-METHYLTETRAHYDROFOLATE CORRINOID/IRON SULFUR PROTEIN METHYLTRANSFERASE | ||||||
![]() | TRANSFERASE / carbon dioxide fixation / cobalamin / methyltatrahydrofolate / methyltransferase / one-carbon metabolism / TIM barrel / homodimer | ||||||
Function / homology | ![]() 5-methyltetrahydrofolate-corrinoid/iron-sulfur protein Co-methyltransferase / methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity / methionine synthase activity / homocysteine metabolic process / carbon fixation / cobalamin binding / tetrahydrofolate metabolic process / methyltransferase activity / methylation / calcium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Doukov, T.I. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W. | ||||||
![]() | ![]() Title: Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Authors: Doukov, T. / Seravalli, J. / Stezowski, J.J. / Ragsdale, S.W. #1: ![]() Title: Preliminary X-ray Crystallographic Study of Methyltetrahydrofolate: Corrinoid/Iron-Sulfur Protein Methyltransferase from Clostridium thermoaceticum Authors: Doukov, T.I. / Zhao, S. / Ross II, C.R. / Roberts, D.L. / Kim, J.J. / Ragsdale, S.W. / Stezowski, J.J. #2: ![]() Title: The Reductive Acetyl Coenzyme A Pathway: Sequence and Heterologous Expression of Active Methyltetrahydrofolate:Corrinoid/Iron-Sulfur Protein Methyltransferase from Clostridium thermoaceticum Authors: Roberts, D.L. / Zhao, S. / Doukov, T. / Ragsdale, S.W. #3: ![]() Title: Binding of (6R,S)-Methyltetrahydrofolate to Methyltransferase from Clostridium thermoaceticum: Role of Protonation of Methyltetrahydrofolate in the Mechanism of Methyl Transfer Authors: Seravalli, J. / Shoemaker, R.K. / Sudbeck, M.L. / Ragsdale, S.W. #4: ![]() Title: Mechanism of Transfer of the Methyl Group from (6S)-Methyltetrahydrofolate to the Corrinoid/Iron-Sulfur Protein Catalyzed by the Methyltransferase from Clostridium thermoaceticum: A Key Step ...Title: Mechanism of Transfer of the Methyl Group from (6S)-Methyltetrahydrofolate to the Corrinoid/Iron-Sulfur Protein Catalyzed by the Methyltransferase from Clostridium thermoaceticum: A Key Step in the Wood-Ljungdahl Pathway of Acetyl-CoA Synthesis Authors: Seravalli, J. / Zhao, S. / Ragsdale, S.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.3 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28670.229 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 57.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 9-15% PEGmme 5000, 20% Glycerol, 50 mM HEPES pH 7.5, 20-50 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Details: used seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 12, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→7 Å / Num. all: 34455 / Num. obs: 28189 / % possible obs: 81.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.294 / % possible all: 87.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO / Resolution: 2.2→7 Å / Num. parameters: 1650 / Num. restraintsaints: 1601 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4125 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.2306 / Rfactor Rwork: 0.2064 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|