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- PDB-2o2r: Crystal structure of the C-terminal domain of rat 10'formyltetrah... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o2r | ||||||
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Title | Crystal structure of the C-terminal domain of rat 10'formyltetrahydrofolate dehydrogenase in complex with NADPH | ||||||
![]() | Formyltetrahydrofolate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / FDH | ||||||
Function / homology | ![]() Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / bile acid signaling pathway / folic acid metabolic process ...Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / bile acid signaling pathway / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / protein-containing complex binding / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsybovsky, Y. / Donato, H. / Krupenko, N.I. / Davies, C. / Krupenko, S.A. | ||||||
![]() | ![]() Title: Crystal structures of the carboxyl terminal domain of rat 10-formyltetrahydrofolate dehydrogenase: implications for the catalytic mechanism of aldehyde dehydrogenases. Authors: Tsybovsky, Y. / Donato, H. / Krupenko, N.I. / Davies, C. / Krupenko, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410 KB | Display | ![]() |
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PDB format | ![]() | 334.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 77.4 KB | Display | |
Data in CIF | ![]() | 110.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2o2pC ![]() 2o2qSC 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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2 | ![]()
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Unit cell |
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Details | The biological unit is the tetramer |
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Components
#1: Protein | Mass: 56621.547 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 397-902 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q5HZB2, UniProt: P28037*PLUS, formyltetrahydrofolate dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6 M AMMONIUM SULPHATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 226906 / Num. obs: 226906 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.7 / Num. unique all: 24034 / Rsym value: 0.506 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2O2Q Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.251 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.126 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Total num. of bins used: 20
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