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- PDB-4ts4: Crystal structure of the hydrolase domain of 10-formyltetrahydrof... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ts4 | ||||||||||||||||||||||||
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Title | Crystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (wild-type) from zebrafish | ||||||||||||||||||||||||
![]() | 10-formyltetrahydrofolate dehydrogenase | ||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / 10-Formyltetrahydrofolate dehydrogenase / hydrolase domain / catalysis | ||||||||||||||||||||||||
Function / homology | ![]() neuromast deposition / Metabolism of folate and pterines / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / embryonic viscerocranium morphogenesis / aldehyde dehydrogenase (NAD+) activity / neural crest cell migration / biosynthetic process / gastrulation ...neuromast deposition / Metabolism of folate and pterines / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / embryonic viscerocranium morphogenesis / aldehyde dehydrogenase (NAD+) activity / neural crest cell migration / biosynthetic process / gastrulation / one-carbon metabolic process / heart development / hydrolase activity / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Lin, C.C. / Chen, C.J. / Fu, T.F. / Chuankhayan, P. / Kao, T.T. / Chang, W.N. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition. Authors: Lin, C.C. / Chuankhayan, P. / Chang, W.N. / Kao, T.T. / Guan, H.H. / Fun, H.K. / Nakagawa, A. / Fu, T.F. / Chen, C.J. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.8 KB | Display | ![]() |
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PDB format | ![]() | 155.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
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Full document | ![]() | 440.3 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qpcC ![]() 4qpdC ![]() 4r8vC ![]() 4tt8C ![]() 4ttsC ![]() 1s3iS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 35456.438 Da / Num. of mol.: 1 / Fragment: UNP residues 1-311 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: E3NZ06, formyltetrahydrofolate dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Bis-Tris (0.1~0.2 M, pH 5.5) and PEG3350 (25~29%, w/v) PH range: 5.5 - 6.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 35347 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4 / % possible all: 99.9 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 1s3i Resolution: 1.75→24.025 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.776 Å2 / ksol: 0.347 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→24.025 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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