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- PDB-5vtm: The crystal structure of minor pseudopilin ternary complex of Xcp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vtm | ||||||
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Title | The crystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2 secretion system of Pseudomonas aeruginosa | ||||||
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![]() | TRANSPORT PROTEIN / Type 2 secretion system | ||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Jia, Z. | ||||||
![]() | ![]() Title: Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa. Authors: Zhang, Y. / Faucher, F. / Zhang, W. / Wang, S. / Neville, N. / Poole, K. / Zheng, J. / Jia, Z. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.8 KB | Display | ![]() |
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PDB format | ![]() | 93.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 453.4 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bw0SC ![]() 3ci0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22247.691 Da / Num. of mol.: 1 / Fragment: residues 44-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: xcpW, pddD, PA3098 / Production host: ![]() ![]() | ||
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#2: Protein | Mass: 30659.467 Da / Num. of mol.: 1 / Fragment: residues 44-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: xcpX, PA3097 / Production host: ![]() ![]() | ||
#3: Protein | Mass: 10534.801 Da / Num. of mol.: 1 / Fragment: residues 38-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: xcpV, pddC, PA3099 / Production host: ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.81 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.5 Details: 19 %-22 % PEG 2000 MME, 0.1M Tris, pH 8.0-9.0, 0.2 M trimethylamine N-oxide PH range: 8.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.51 Å / Num. obs: 31625 / % possible obs: 99.2 % / Redundancy: 9.8 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Net I/σ(I): 10.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BW0, 3CI0 Resolution: 2.041→43.51 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.041→43.51 Å
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Refine LS restraints |
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LS refinement shell |
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