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- PDB-3apy: Properties and crystal structure of methylenetetrahydrofolate red... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3apy | ||||||
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Title | Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8 | ||||||
![]() | Methylenetetrahydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / TIM BARREL / FLAVIN | ||||||
Function / homology | ![]() methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, K. | ||||||
![]() | ![]() Title: Properties and Crystal Structure of Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8. Authors: Igari, S. / Ohtaki, A. / Yamanaka, Y. / Sato, Y. / Yohda, M. / Odaka, M. / Noguchi, K. / Yamada, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 480.6 KB | Display | ![]() |
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PDB format | ![]() | 395.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 97.2 KB | Display | |
Data in CIF | ![]() | 132.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aptC ![]() 1v93S 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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Unit cell |
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Components
#1: Protein | Mass: 34648.680 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: pET(tMRwt) / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H] #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, 0.2M Ammonium Sulfate, 20-25% PEG 4000, 5% GLYCEROL , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2010 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→19.96 Å / Num. obs: 72447 / % possible obs: 91.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V93 Resolution: 2.8→19.96 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.873 / Rfactor Rfree error: 0.29767 / SU B: 17.619 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.499 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
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