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- PDB-5ybi: Structure of the bacterial pathogens ATPase with substrate AMPPNP -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ybi | ||||||||||||
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Title | Structure of the bacterial pathogens ATPase with substrate AMPPNP | ||||||||||||
![]() | Probable ATP synthase SpaL/MxiB | ||||||||||||
![]() | HYDROLASE / ATPase / T3SS / hexamer / AMPPNP | ||||||||||||
Function / homology | ![]() protein-exporting ATPase activity / protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mu, Z.X. / Gao, X.P. / Cui, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri. Authors: Gao, X. / Mu, Z. / Yu, X. / Qin, B. / Wojdyla, J. / Wang, M. / Cui, 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 | ![]() | 278.6 KB | Display | ![]() |
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PDB format | ![]() | 227.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.3 KB | Display | ![]() |
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Full document | ![]() | 763.8 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ybhSC ![]() 5zt1C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41181.637 Da / Num. of mol.: 2 / Fragment: UNP residues 84-430 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0A1C1, H+-transporting two-sector ATPase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ANP / | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density meas: 0.01 Mg/m3 / Density % sol: 54.9 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 0.1M Bicine, pH8.6, 1.2M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2013 |
Radiation | Monochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97876 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.4 Å / Num. obs: 82611 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.52 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.56 |
Reflection shell | Resolution: 2.2→2.41 Å / Redundancy: 8.44 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.27 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YBH Resolution: 2.268→43 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.268→43 Å
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Refine LS restraints |
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LS refinement shell |
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