+Open data
-Basic information
Entry | Database: PDB / ID: 3hy3 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human MTHFS with 10-formyltetrahydrofolate | ||||||
Components | 5-formyltetrahydrofolate cyclo-ligase | ||||||
Keywords | LIGASE / antifolate / cancer / 10-formyltetrahydrofolate / ATP-binding / Folate-binding / Magnesium / Nucleotide-binding | ||||||
Function / homology | Function and homology information folic acid catabolic process / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / folic acid-containing compound biosynthetic process / formate metabolic process / glutamate metabolic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid binding ...folic acid catabolic process / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / folic acid-containing compound biosynthetic process / formate metabolic process / glutamate metabolic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid binding / folic acid metabolic process / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wu, D. / Li, Y. / Song, G. / Cheng, C. / Shaw, N. / Liu, Z.-J. | ||||||
Citation | Journal: Cancer Res. / Year: 2009 Title: Structural basis for the inhibition of human 5,10-methenyltetrahydrofolate synthetase by N10-substituted folate analogues Authors: Wu, D. / Li, Y. / Song, G. / Cheng, C. / Zhang, R. / Joachimiak, A. / Shaw, N. / Liu, Z.-J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hy3.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hy3.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/3hy3 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/3hy3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3hxtSC 3hy4C 3hy6C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 23289.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MTHFS / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P49914, 5-formyltetrahydrofolate cyclo-ligase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-10F / | ||||
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 100mM HEPES, pH6.6, 20mM MgCl2.6H2O, 20mM NiCl2.6H2O, 20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 23583 / Num. obs: 23512 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HXT Resolution: 1.8→46.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.938 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS: THE LIGAND 10F IN THIS ENTRY IS 10-FORMYLTETRAHYDROFOLATE. HOWEVER, THERE IS SOME DISCREPANCY IN THE GEOMETRY. THE GEOMETRY FOR 10F IS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS: THE LIGAND 10F IN THIS ENTRY IS 10-FORMYLTETRAHYDROFOLATE. HOWEVER, THERE IS SOME DISCREPANCY IN THE GEOMETRY. THE GEOMETRY FOR 10F IS SUGGESTED BY THE REFINEMENT. THE CO-ORDINATES FIT WELL IN THE ELECTRON DENSITY MAP. THE MAP WAS GENERATED USING A DATASET COLLECTED AT 1.8 ANGSTROM RESOLUTION. THE DENSITY FOR THE LIGAND IS UNAMBIGUOUS AND THEREFORE THE GEOMETRIES ARE CORRECT AND ARE AS THEY WOULD BE IN A BIOLOGICAL MOLECULE, WHERE THE MICRO ENVIRONMENT HAS A PROFOUND INFLUENCE ON THE GEOMETRIES OF THE LIGAND.
| |||||||||||||||||||||||||
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: 26.119 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.3 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|