[English] 日本語
Yorodumi- PDB-8szd: Crystal structure of Yersinia pestis dihydrofolate reductase at 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8szd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Yersinia pestis dihydrofolate reductase at 1.25-A resolution | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / DHFR | ||||||
Function / homology | Function and homology information dihydrofolate metabolic 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: 1.25 Å | ||||||
Authors | Shaw, G.X. / Cherry, S. / Tropea, J.E. / Waugh, D.S. / Ji, X. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To be published Title: Crystal structure of Yersinia pestis dihydrofolate reductase at 1.25-A resolution Authors: Shaw, G.X. / Cherry, S. / Tropea, J.E. / Waugh, D.S. / Ji, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8szd.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8szd.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 8szd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8szd_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8szd_full_validation.pdf.gz | 439 KB | Display | |
Data in XML | 8szd_validation.xml.gz | 10 KB | Display | |
Data in CIF | 8szd_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/8szd ftp://data.pdbj.org/pub/pdb/validation_reports/sz/8szd | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 18336.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: folA, tmrA, YPO0486 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N4BLI0, dihydrofolate reductase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.21 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulfate, citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2006 / Details: Double crystal | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→30 Å / Num. obs: 40606 / % possible obs: 95 % / Redundancy: 5.1 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.03 / Rrim(I) all: 0.07 / Χ2: 0.919 / Net I/σ(I): 18 / Num. measured all: 208976 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→27.29 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.42 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→27.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|