[English] 日本語
Yorodumi- PDB-3q1h: Crystal Structure of Dihydrofolate Reductase from Yersinia pestis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q1h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Dihydrofolate Reductase from Yersinia pestis | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta fold / cytosol | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Dihydrofolate Reductase from Yersinia pestis Authors: Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3q1h.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3q1h.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 3q1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/3q1h ftp://data.pdbj.org/pub/pdb/validation_reports/q1/3q1h | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ddsS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 18350.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: folA, y3688, YPO0486, YP_3693 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRXpGro7 References: UniProt: Q7CG83, UniProt: A0A3N4BLI0*PLUS, dihydrofolate reductase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.68 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium Sulfate, 0.1M Bis-Tris pH5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 14518 / Num. obs: 14518 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.88 / Num. unique all: 640 / Rsym value: 0.393 / % possible all: 89 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBID 1DDS Resolution: 1.804→33.759 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.421 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.804→33.759 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 15.8425 Å / Origin y: -12.2798 Å / Origin z: 13.0938 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain A |