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Yorodumi- PDB-2hwg: Structure of phosphorylated Enzyme I of the phosphoenolpyruvate:s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hwg | ||||||
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Title | Structure of phosphorylated Enzyme I of the phosphoenolpyruvate:sugar phosphotransferase system | ||||||
Components | Phosphoenolpyruvate-protein phosphotransferasePhosphoenolpyruvate—protein phosphotransferase | ||||||
Keywords | TRANSFERASE / enzyme I / phosphoenolpyruvate:sugar phosphotransferase system / PTS | ||||||
Function / homology | Function and homology information phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Lim, K. / Teplyakov, A. / Herzberg, O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein. Authors: Teplyakov, A. / Lim, K. / Zhu, P.P. / Kapadia, G. / Chen, C.C. / Schwartz, J. / Howard, A. / Reddy, P.T. / Peterkofsky, A. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hwg.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hwg.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hwg ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hwg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The dimer in the asymmetric unit is the biological assembly. |
-Components
#1: Protein | Mass: 64558.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsI / Plasmid: pRE1 / Production host: Escherichia coli (E. coli) References: UniProt: P08839, phosphoenolpyruvate-protein phosphotransferase #2: Chemical | #3: Chemical | #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: 2.51 Å3/Da / Density % sol: 50.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: The protein sample (10 mg/mL) was mixed with MgCl2 and PEP to bring each additive to a final concentration of 10 mM. After ~5 min, sodium oxalate was added to a final concentration of 10 mM. ...Details: The protein sample (10 mg/mL) was mixed with MgCl2 and PEP to bring each additive to a final concentration of 10 mM. After ~5 min, sodium oxalate was added to a final concentration of 10 mM. Drops containing 1:1 protein and reservoir solution were equilibrated against reservoir solution containing 22% w/v polyethylene glycol 6000, 2% saturated ammonium sulfate, and 100 mM Na+HEPES., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9793 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2000 / Details: mirrors |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 36262 / Num. obs: 36262 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.326 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1zym,2bg5 Resolution: 2.7→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.264 |