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Yorodumi- PDB-6fnu: Structure of S. cerevisiae Methylenetetrahydrofolate reductase 1,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fnu | ||||||
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Title | Structure of S. cerevisiae Methylenetetrahydrofolate reductase 1, catalytic domain | ||||||
Components | Methylenetetrahydrofolate reductase 1 | ||||||
Keywords | OXIDOREDUCTASE / reductase / one carbon metabolism / TIM barrel / folate metabolism / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate reductase [NAD(P)H] / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NADH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Kopec, J. / Rembeza, E. / Bezerra, G.A. / Newman, J. / Bountra, C. / Froese, D.S. / Baumgartner, M. / Yue, W.W. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Authors: Froese, D.S. / Kopec, J. / Rembeza, E. / Bezerra, G.A. / Oberholzer, A.E. / Suormala, T. / Lutz, S. / Chalk, R. / Borkowska, O. / Baumgartner, M.R. / Yue, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fnu.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fnu.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/6fnu ftp://data.pdbj.org/pub/pdb/validation_reports/fn/6fnu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34794.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MET12, YPL023C, LPB8C / Production host: Escherichia coli (E. coli) References: UniProt: P46151, methylenetetrahydrofolate reductase [NAD(P)H] |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium/potassium tartrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→61.76 Å / Num. obs: 53602 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rpim(I) all: 0.066 / Rrim(I) all: 0.191 / Net I/σ(I): 11.4 / Num. measured all: 270864 |
Reflection shell | Resolution: 1.56→1.59 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.3 / Num. measured all: 12175 / Num. unique obs: 1643 / CC1/2: 0.523 / Rpim(I) all: 0.534 / Rrim(I) all: 1.593 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→22.75 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.46 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.46 Å2 / Biso mean: 19.947 Å2 / Biso min: 9.41 Å2
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Refinement step | Cycle: final / Resolution: 1.56→22.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.9622 Å / Origin y: 4.6623 Å / Origin z: 15.7046 Å
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