+Open data
-Basic information
Entry | Database: PDB / ID: 1jde | ||||||
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Title | K22A mutant of pyruvate, phosphate dikinase | ||||||
Components | PYRUVATE, PHOSPHATE DIKINASE | ||||||
Keywords | TRANSFERASE / PHOSPHOTRANSFERASE / KINASE / nucleotide binding site mutant | ||||||
Function / homology | Function and homology information pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium symbiosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Ye, D. / Wei, M. / McGuire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Martin, B.M. / Dunaway-Mariano, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase. Authors: Ye, D. / Wei, M. / McGuire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Martin, B.M. / Dunaway-Mariano, D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Swiveling-domain Mechanism for Enzymatic Phosphotransfer between Remote Reaction Sites Authors: Herzberg, O. / Chen, C.C. / Kapadia, G. / McGuire, M. / Carroll, L.J. / Noh, S.J. / Dunaway-Mariano, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jde.cif.gz | 180.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jde.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jde ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jde | HTTPS FTP |
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-Related structure data
Related structure data | 1dikS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 96582.047 Da / Num. of mol.: 1 / Mutation: K22A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: PODK / Plasmid: PACYC184D-12 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 101 / References: UniProt: P22983, pyruvate, phosphate dikinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50% saturated ammonium sulfate, 100mM Hepes buffer, 100mM KCL, 0.1mM EDTA, 1mM Mercaptoethanol, 20mM imidazole buffer pH 6.5, 10mg/ml protein, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Aug 5, 1996 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 25068 / Num. obs: 25068 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 53 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1DIK without solvent molecules and with K22 truncated to Gly Resolution: 2.8→10 Å / σ(F): 2 / Details: TNT was also used for refinement. /
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.193 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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