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Yorodumi- PDB-2r82: Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r82 | ||||||
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Title | Pyruvate phosphate dikinase (PPDK) triple mutant R219E/E271R/S262D adapts a second conformational state | ||||||
Components | Pyruvate, phosphate dikinase | ||||||
Keywords | TRANSFERASE / phosphotransferase / conformational transition / swiveling domain / remote active sites / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide-binding / Phosphorylation | ||||||
Function / homology | Function and homology information pyruvate, phosphate dikinase / pyruvate, phosphate dikinase activity / pyruvate metabolic process / kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium symbiosum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Lim, K. / Read, R.J. / Chen, C.C. / Herzberg, O. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Swiveling domain mechanism in pyruvate phosphate dikinase. Authors: Lim, K. / Read, R.J. / Chen, C.C. / Tempczyk, A. / Wei, M. / Ye, D. / Wu, C. / Dunaway-Mariano, D. / Herzberg, O. #1: Journal: Biochemistry / Year: 2002 Title: Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis Authors: Herzberg, O. / Chen, C. / Liu, S. / Tempczyk, A. / Howard, A. / Wei, M. / Ye, D. / Dunaway-Mariano, D. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites Authors: Herzberg, O. / Chen, C. / Kapadia, G. / Mcguire, M. / Carroll, L.J. / Noh, S.J. / Dunaway-Mariano, D. #3: Journal: Biochemistry / Year: 1998 Title: Location of the phosphate binding site within Clostridium Symbiosum pyruvate phosphate dikinase Authors: Mcguire, M. / Huang, K. / Kapadia, G. / Herzberg, O. / Dunaway-Mariano, D. #4: Journal: J.Biol.Chem. / Year: 2000 Title: Identification of the domain-domain docking sites within Clostridium Symbiosum pyruvate phosphate dikinase by amino acid replacement Authors: Wei, M. / Li, Z. / Ye, D. / Herzberg, O. / 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 | 2r82.cif.gz | 162.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r82.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 2r82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r82_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 2r82_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 2r82_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 2r82_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/2r82 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r82 | HTTPS FTP |
-Related structure data
Related structure data | 1kblS 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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Unit cell |
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-Components
#1: Protein | Mass: 96799.359 Da / Num. of mol.: 1 / Mutation: R219E, S262D, E271R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: ppdK / Plasmid: pACYC184 D12 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P22983, pyruvate, phosphate dikinase |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.19 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50% saturated ammonium sulfate, 0.1 M Na Hepes, 28 mg/ml protein (in 20 mM imidazole (pH 6.5), 0.1 mM EDTA, 100 mM KCl, and 1mM DTT), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: Harvard mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. all: 11406 / Num. obs: 11406 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.6→3.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.5 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KBL Resolution: 3.6→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 68 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.76 Å / Rfactor Rfree: 0.38 / Rfactor Rwork: 0.35 |