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Yorodumi- PDB-6at3: E. coli phosphoenolpyruvate carboxykinase Y207F mutant bound to t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6at3 | |||||||||
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Title | E. coli phosphoenolpyruvate carboxykinase Y207F mutant bound to thiosulfate and oxaloacetate | |||||||||
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: 1.455 Å | |||||||||
Authors | Tang, H.Y.H. / Shin, D.S. / Tainer, J.A. | |||||||||
Funding support | United States, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6at3.cif.gz | 400.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6at3.ent.gz | 327.3 KB | Display | PDB format |
PDBx/mmJSON format | 6at3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6at3_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
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Full document | 6at3_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 6at3_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 6at3_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6at3 ftp://data.pdbj.org/pub/pdb/validation_reports/at/6at3 | HTTPS FTP |
-Related structure data
Related structure data | 6asiC 6asmC 6asnC 6at2C 6at4C 2olqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60522.066 Da / Num. of mol.: 2 / Mutation: Y207F 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-OAA / | #3: Chemical | ChemComp-THJ / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 24% 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 |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 1.455→47.33 Å / Num. obs: 208965 / % possible obs: 98.68 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08447 / Net I/σ(I): 11.88 |
Reflection shell | Resolution: 1.455→1.507 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.717 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 20200 / CC1/2: 0.457 / % possible all: 94.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OLQ Resolution: 1.455→47.335 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.455→47.335 Å
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Refine LS restraints |
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LS refinement shell |
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