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- PDB-1s3i: Crystal structure of the N terminal hydrolase domain of 10-formyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s3i | ||||||
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Title | Crystal structure of the N terminal hydrolase domain of 10-formyltetrahydrofolate dehydrogenase | ||||||
![]() | 10-formyltetrahydrofolate dehydrogenase | ||||||
![]() | HYDROLASE / OXIDOREDUCTASE / Rossmann fold | ||||||
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 | ![]() ![]() | ||||||
![]() | Chumanevich, A.A. / Krupenko, S.A. / Davies, C. | ||||||
![]() | ![]() Title: The crystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase: mechanism of hydrolysis and its interplay with the dehydrogenase domain. Authors: Chumanevich, A.A. / Krupenko, S.A. / Davies, C. #1: ![]() Title: Crystallization and preliminary X-ray diffraction analysis of recombinant hydrolase domain of 10-formyltetrahydrofolate dehydrogenase Authors: Chumanevich, A.A. / Davies, C. / Krupenko, S.A. | ||||||
History |
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Remark 999 | SEQUENCE THE AMINO ACIDS AT POSITIONS 42, 51, 52, 283, AND 284 CONFLICT WITH THE PUBLISHED SEQUENCE. ...SEQUENCE THE AMINO ACIDS AT POSITIONS 42, 51, 52, 283, AND 284 CONFLICT WITH THE PUBLISHED SEQUENCE. THE ASPARTATE AT POSITION 310 IS NON-NATIVE AND RESULTS FROM THE CLONING. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 447 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 34081.836 Da / Num. of mol.: 1 / Fragment: Nt-FDH,residues 1-310 / Mutation: none Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P28037, formyltetrahydrofolate dehydrogenase | ||
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#2: Chemical | ChemComp-BME / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.09 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.3 M ammonium sulphate, 0.1M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Chumanevich, A.A., (2002) Acta Cryst., D58, 1841. / PH range low: 5.1 / PH range high: 4.9 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 2, 2001 / Details: mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.7 Å / Num. all: 19201 / Num. obs: 19201 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2 / Num. unique all: 1863 / Rsym value: 0.346 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 80514 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 1863 / Num. measured obs: 7894 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.745 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Num. reflection obs: 18079 / % reflection Rfree: 5 % / Rfactor Rfree: 0.305 / Rfactor Rwork: 0.242 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å |