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- PDB-4cii: Crystal structure of N-terminally truncated Helicobacter pylori T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cii | ||||||
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Title | Crystal structure of N-terminally truncated Helicobacter pylori T4SS Protein CagL as domain swapped dimer | ||||||
![]() | CAG PATHOGENICITY ISLAND PROTEIN (CAG18) | ||||||
![]() | PROTEIN BINDING / ADHESION / RGD MOTIF / INTEGRIN BINDING / TYPE IV SECRETION / T4S / VIRULENCE / HP0539 | ||||||
Function / homology | Cag pathogenicity island protein (Cag18)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barden, S. / Schomburg, B. / Niemann, H.H. | ||||||
![]() | ![]() Title: Structure of a Three-Dimensional Domain-Swapped Dimer of the Helicobacter Pylori Type Iv Secretion System Pilus Protein Cagl. Authors: Barden, S. / Schomburg, B. / Conradi, J. / Backert, S. / Sewald, N. / Niemann, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.9 KB | Display | ![]() |
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Full document | ![]() | 438.2 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cziS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25747.236 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-237 Source method: isolated from a genetically manipulated source Details: FRAGMENT OF UNSPECIFIC N-TERMINAL PROTEOLYSIS OF CAGL(AA21-237)-LEHHHHHH IN THE CRYSTALLISATION DROP Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MRD / ( |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINALLY |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.6 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4.2 Details: 100 MM CITRATE/PHOSPHATE PH 4.2, 40% (V/V) 2-METHYL-2,4-PENTANEDIOL, 6.4% TERT-BUTANOL. VAPOR DIFFUSION AT 277 K WITH DROP RATIO OF 2:1 PROTEIN TO RESERVOIR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→44.75 Å / Num. obs: 16080 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CZI Resolution: 2.15→40.282 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 24.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→40.282 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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