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- PDB-7lkq: The PilZ(delta107-117)-FimX(GGDEF-EAL) complex from Xanthomonas citri -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lkq | ||||||
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Title | The PilZ(delta107-117)-FimX(GGDEF-EAL) complex from Xanthomonas citri | ||||||
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![]() | TRANSPORT PROTEIN / Type IV pilus | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Llontop, E.E. / Guzzo, C.R. / Farah, C.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The PilB-PilZ-FimX regulatory complex of the Type IV pilus from Xanthomonas citri. Authors: Llontop, E.E. / Cenens, W. / Favaro, D.C. / Sgro, G.G. / Salinas, R.K. / Guzzo, C.R. / Farah, C.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.6 KB | Display | ![]() |
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PDB format | ![]() | 62.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 797.1 KB | Display | ![]() |
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Full document | ![]() | 803.1 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lkmC ![]() 7lknC ![]() 7lkoC ![]() 4fouS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47794.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FimX residues 255-689 (contains both GGDEF and EAL domains) preceeded by 21 residue N-terminal sequence containing 6XHis-tag. No electron density observed for GGDEF domain. Source: (gene. exp.) ![]() Strain: 306 / Gene: XAC2398 / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 11228.033 Da / Num. of mol.: 1 Mutation: lacking residues 107-117 compared to the native protein Source method: isolated from a genetically manipulated source Details: PilZ residues 1-106 (lacking residues 107-117) Source: (gene. exp.) ![]() Strain: 306 / Gene: pilZ, XAC1133 / Production host: ![]() ![]() | ||||
#3: Chemical | ChemComp-C2E / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MG / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 10 mg/ml protein, 0.1 M MES pH 6.5, 1.6 M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 9964 / % possible obs: 99.96 % / Redundancy: 13.6 % / Biso Wilson estimate: 95.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3.4→3.74 Å / Redundancy: 14 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2287 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FOU Resolution: 3.4→49.79 Å / SU ML: 0.4971 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.0654 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.44 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→49.79 Å
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Refine LS restraints |
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LS refinement shell |
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