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- PDB-7xlf: Crystal structure of CH3-THF complex of methylenetetrahydrofolate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xlf | ||||||
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Title | Crystal structure of CH3-THF complex of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6 | ||||||
![]() | 5,10-methylenetetrahydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / CH3-THF oxidation / Non-NADH/NAD+ binding type / TIM barrel / FLAVOPROTEIN | ||||||
Function / homology | ![]() methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine metabolic process / tetrahydrofolate interconversion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, H.Y. / Senda, M. / Senda, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6 Authors: Yu, H.Y. / Senda, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
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PDB format | ![]() | 99.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xg9SC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 31362.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: G2IQS8, methylenetetrahydrofolate reductase [NAD(P)H] #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 20% (w/v) PEG 4000, 0.1 M sodium citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.7 Å / Num. obs: 46088 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.73 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.064 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.853 / Num. unique obs: 2827 / CC1/2: 0.727 / Rpim(I) all: 0.537 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7XG9 Resolution: 1.85→38.88 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1217 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→38.88 Å
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Refine LS restraints |
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LS refinement shell |
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