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Yorodumi- PDB-7pva: 1.9 Angstrom crystal structure of dimeric PorX, co-crystallized i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pva | |||||||||
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Title | 1.9 Angstrom crystal structure of dimeric PorX, co-crystallized in the presence of zinc | |||||||||
Components | Response regulator | |||||||||
Keywords | SIGNALING PROTEIN / Response regulator / Type 9 Secretion System / PglZ / Phosphodiesterase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Porphyromonas gingivalis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | |||||||||
Authors | Schmitz, C.A. / Madej, M. / Potempa, J. / Sola, M. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors. Authors: Schmitz, C. / Madej, M. / Nowakowska, Z. / Cuppari, A. / Jacula, A. / Ksiazek, M. / Mikruta, K. / Wisniewski, J. / Pudelko-Malik, N. / Saran, A. / Zeytuni, N. / Mlynarz, P. / Lamont, R.J. / ...Authors: Schmitz, C. / Madej, M. / Nowakowska, Z. / Cuppari, A. / Jacula, A. / Ksiazek, M. / Mikruta, K. / Wisniewski, J. / Pudelko-Malik, N. / Saran, A. / Zeytuni, N. / Mlynarz, P. / Lamont, R.J. / Uson, I. / Siksnys, V. / Potempa, J. / Sola, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pva.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pva.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7pva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pva_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
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Full document | 7pva_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 7pva_validation.xml.gz | 95.7 KB | Display | |
Data in CIF | 7pva_validation.cif.gz | 143.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/7pva ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pva | HTTPS FTP |
-Related structure data
Related structure data | 7pv7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 62136.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria) Strain: ATCC BAA-308 / W83 / Gene: PG_0928 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MVV4 |
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-Non-polymers , 7 types, 1886 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-BEF / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-FMT / #7: Chemical | #8: 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: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM glycine pH 8.0, 100 mM sodium formate and 4% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.28202 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28202 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→68.59 Å / Num. obs: 186912 / % possible obs: 98.3 % / Redundancy: 16.9 % / Biso Wilson estimate: 40.57 Å2 / CC1/2: 0.998 / CC star: 1 / Rpim(I) all: 0.03758 / Net I/σ(I): 12.29 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 17 % / Num. unique obs: 18467 / CC1/2: 0.609 / CC star: 0.87 / Rpim(I) all: 0.7175 / % possible all: 96.75 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→68.59 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 230.17 Å2 / Biso mean: 63.302 Å2 / Biso min: 23.95 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→68.59 Å
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