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Yorodumi- PDB-5zt1: Structure of the bacterial pathogens ATPase with substrate ATP gamma S -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zt1 | |||||||||
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Title | Structure of the bacterial pathogens ATPase with substrate ATP gamma S | |||||||||
Components | Probable ATP synthase SpaL/MxiB | |||||||||
Keywords | HYDROLASE / ATPase / T3SS / hexamer / ATP gamma S | |||||||||
Function / homology | Function and homology information 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 | Shigella flexneri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.114 Å | |||||||||
Authors | Gao, X.P. / Mu, Z.X. / Cui, S. | |||||||||
Funding support | China, 2items
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Citation | Journal: Front Microbiol / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zt1.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zt1.ent.gz | 213.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zt1_validation.pdf.gz | 554.1 KB | Display | wwPDB validaton report |
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Full document | 5zt1_full_validation.pdf.gz | 565.7 KB | Display | |
Data in XML | 5zt1_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 5zt1_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/5zt1 ftp://data.pdbj.org/pub/pdb/validation_reports/zt/5zt1 | HTTPS FTP |
-Related structure data
Related structure data | 5ybhC 5ybiC 2oblS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaL, mxiB, spa47, CP0149 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: P0A1C1, H+-transporting two-sector ATPase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-AGS / | |
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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: 2.67 Å3/Da / Density meas: 0.01 Mg/m3 / Density % sol: 54 % 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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97876 Å |
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: 3.1→50 Å / Num. obs: 16927 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.43 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 17.78 |
Reflection shell | Resolution: 3.11→3.3 Å / Redundancy: 8.86 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 5.23 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2obl Resolution: 3.114→29.868 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.78 Details: Authors state that the low occupancy of the ligands result from only fewer protein molecules bound ligands.we balanced B-factors and occupancy of ligands when refinement. SF FILE CONTAINS ...Details: Authors state that the low occupancy of the ligands result from only fewer protein molecules bound ligands.we balanced B-factors and occupancy of ligands when refinement. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.114→29.868 Å
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Refine LS restraints |
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LS refinement shell |
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