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- PDB-5voo: Methionine synthase folate-binding domain with methyltetrahydrofo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5voo | ||||||
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Title | Methionine synthase folate-binding domain with methyltetrahydrofolate from Thermus thermophilus HB8 | ||||||
![]() | 5-methyltetrahydrofolate homocysteine S-methyltransferase | ||||||
![]() | TRANSFERASE / METHYLTRANSFERASE / pterin binding / B12 binding / OXIDOREDUCTASE | ||||||
Function / homology | ![]() methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koutmos, M. / Yamada, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'. Authors: Yamada, K. / Koutmos, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 617.9 KB | Display | ![]() |
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PDB format | ![]() | 525.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 61.8 KB | Display | |
Data in CIF | ![]() | 82.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vonSC ![]() 5vopC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 33016.051 Da / Num. of mol.: 6 / Fragment: folate-binding domain residues 353-648 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0618 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 340 molecules ![](data/chem/img/C2F.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-C2F / #3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium citrate pH 4.5, 22 % polyethylene glycol 3350, 0.2 M tri-sodium citrate, soaked with 6S-methyltetrahydrofolate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2016 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→163.21 Å / Num. obs: 100615 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.048 / Net I/σ(I): 8.93 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 4857 / CC1/2: 0.651 / Rpim(I) all: 0.342 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VON Resolution: 2.4→163.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.356 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.272 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→163.21 Å
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Refine LS restraints |
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