[English] 日本語
Yorodumi- PDB-4pss: Multiconformer model for Escherichia coli dihydrofolate reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pss | ||||||
---|---|---|---|---|---|---|---|
Title | Multiconformer model for Escherichia coli dihydrofolate reductase at 100K | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / reductase | ||||||
Function / homology | Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / FOLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.849 Å | ||||||
Authors | Keedy, D.A. / van den Bedem, H. / Sivak, D.A. / Petsko, G.A. / Ringe, D. / Wilson, M.A. / Fraser, J.S. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR. Authors: Keedy, D.A. / van den Bedem, H. / Sivak, D.A. / Petsko, G.A. / Ringe, D. / Wilson, M.A. / Fraser, J.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pss.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pss.ent.gz | 175.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pss_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4pss_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4pss_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4pss_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4pss ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4pss | HTTPS FTP |
-Related structure data
Related structure data | 4p3qC 4p3rC 4pstC 4pthC 4ptjC 1rx2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18051.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BN896_0046, folA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N356 | ||
---|---|---|---|
#2: Chemical | ChemComp-FOL / | ||
#3: Chemical | ChemComp-NAP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.62 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 7 Details: 17% PEG 400, 20 mM imidazole pH 7.0, 125 mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.849→40.78 Å / Num. obs: 130200 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 7.68 Å2 / Rsym value: 0.049 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 0.85→0.88 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 97.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RX2 Resolution: 0.849→40.78 Å / SU ML: 0.09 / σ(F): 1.34 / Phase error: 16.44 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.849→40.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|