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Yorodumi- PDB-6pc2: Crystal structure of Helicobacter pylori PPX/GppA in complex with GNP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pc2 | ||||||
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Title | Crystal structure of Helicobacter pylori PPX/GppA in complex with GNP | ||||||
Components | Guanosine pentaphosphate phosphohydrolase | ||||||
Keywords | HYDROLASE / pppGpp / ppGpp / PPX / GppA / Polyphosphate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Song, H. / Wang, C. / Shaw, G.X. / Ji, X. | ||||||
Citation | Journal: Febs J. / Year: 2020 Title: Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. Authors: Song, H. / Dharmasena, M.N. / Wang, C. / Shaw, G.X. / Cherry, S. / Tropea, J.E. / Jin, D.J. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pc2.cif.gz | 205.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pc2.ent.gz | 160.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/6pc2 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/6pc2 | HTTPS FTP |
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-Related structure data
Related structure data | 6pbzC 6pc0C 6pc1C 6pc3C 3hi0S 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: 55655.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria) Strain: G27 / Gene: HPG27_257 / Production host: Escherichia coli (E. coli) / References: UniProt: B5ZA44 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2016 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. obs: 23947 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.055 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2375 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3hi0 Resolution: 2.9→35.884 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→35.884 Å
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Refine LS restraints |
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LS refinement shell |
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