+Open data
-Basic information
Entry | Database: PDB / ID: 6at4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate | |||||||||
Components | Phosphoenolpyruvate carboxykinase (ATP) | |||||||||
Keywords | LYASE / Nonnative ligand | |||||||||
Function / homology | Function and homology information phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / calcium ion binding / magnesium ion binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.332 Å | |||||||||
Authors | Tang, H.Y.H. / Shin, D.S. / Tainer, J.A. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Structural Control of Nonnative Ligand Binding in Engineered Mutants of Phosphoenolpyruvate Carboxykinase. Authors: Tang, H.Y.H. / Shin, D.S. / Hura, G.L. / Yang, Y. / Hu, X. / Lightstone, F.C. / McGee, M.D. / Padgett, H.S. / Yannone, S.M. / Tainer, J.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6at4.cif.gz | 600.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6at4.ent.gz | 502.9 KB | Display | PDB format |
PDBx/mmJSON format | 6at4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6at4_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6at4_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6at4_validation.xml.gz | 45.3 KB | Display | |
Data in CIF | 6at4_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6at4 ftp://data.pdbj.org/pub/pdb/validation_reports/at/6at4 | HTTPS FTP |
-Related structure data
Related structure data | 6asiC 6asmC 6asnC 6at2C 6at3C 2olqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60538.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pckA, pck, b3403, JW3366 / Production host: Escherichia coli (E. coli) References: UniProt: P22259, phosphoenolpyruvate carboxykinase (ATP) #2: Chemical | ChemComp-THJ / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 1.332→119.156 Å / Num. obs: 470294 / % possible obs: 90.7 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.78 |
Reflection shell | Resolution: 1.332→1.4 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1 / Num. unique obs: 48895 / CC1/2: 0.436 / % possible all: 58.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OLQ Resolution: 1.332→78.188 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.39
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.332→78.188 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|