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Yorodumi- PDB-8cb2: A complex of cagX and cagY components of Helicobacter pylori type... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cb2 | ||||||
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Title | A complex of cagX and cagY components of Helicobacter pylori type IV secretion system | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Helicobacter pylori / CagX_CTD / CagY_CTD / complex structure / interaction | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Isupov, M.N. / Jiang, M. / Zhang, H. / Wu, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: A complex of cagX and cagY components of Helicobacter pylori type IV secretion system Authors: Isupov, M.N. / Jiang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cb2.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cb2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cb2_validation.pdf.gz | 746.5 KB | Display | wwPDB validaton report |
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Full document | 8cb2_full_validation.pdf.gz | 754.1 KB | Display | |
Data in XML | 8cb2_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 8cb2_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/8cb2 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/8cb2 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: End auth comp-ID: LEU / End label comp-ID: LEU
NCS ensembles :
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-Components
#1: Protein | Mass: 19163.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q75X32 #2: Protein | Mass: 28513.678 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: cagY / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A438QIF3 #3: Chemical | ChemComp-CA / | #4: 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: 3.15 Å3/Da / Density % sol: 60.91 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion Details: 0.2M Calcium acetate, 0.1M Bis-tris pH 5.5 and 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9689 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9689 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.08 Å / Num. obs: 30397 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.99 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.7→2.83 Å / Num. unique obs: 3985 / CC1/2: 0.241 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→49.079 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.43 / SU ML: 0.436 / Cross valid method: FREE R-VALUE / ESU R: 0.781 / ESU R Free: 0.374 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 109.063 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→49.079 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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