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Yorodumi- PDB-6pc3: Crystal structure of Helicobacter pylori PPX/GppA in complex with GSP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pc3 | ||||||
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Title | Crystal structure of Helicobacter pylori PPX/GppA in complex with GSP | ||||||
Components | Guanosine pentaphosphate phosphohydrolase | ||||||
Keywords | HYDROLASE / pppGpp / ppGpp / PPX / GppA / Polyphosphate | ||||||
Function / homology | Function and homology information guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity / nucleobase-containing small molecule interconversion / regulation of transcription by RNA polymerase II / metal ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 6pc3.cif.gz | 222 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pc3.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pc3_validation.pdf.gz | 4.2 MB | Display | wwPDB validaton report |
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Full document | 6pc3_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 6pc3_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 6pc3_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/6pc3 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/6pc3 | HTTPS FTP |
-Related structure data
Related structure data | 6pbzC 6pc0C 6pc1C 6pc2C 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 8 types, 454 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
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: 2.35 Å3/Da / Density % sol: 47.68 % |
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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: Aug 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 60029 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rpim(I) all: 0.061 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5951 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3hi0 Resolution: 2.1→45.428 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.428 Å
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Refine LS restraints |
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LS refinement shell |
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