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Yorodumi- PDB-1g6o: CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI ATPASE, HP0525, IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g6o | ||||||
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Title | CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI ATPASE, HP0525, IN COMPLEX WITH ADP | ||||||
Components | CAG-ALPHA | ||||||
Keywords | HYDROLASE / ATPase / type IV secretion system / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information secretion by the type IV secretion system / type IV secretion system complex / nucleotide binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Yeo, H.J. / Savvides, S.N. / Herr, A.B. / Lanka, E. / Waksman, G. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Crystal structure of the hexameric traffic ATPase of the Helicobacter pylori type IV secretion system. Authors: Yeo, H.J. / Savvides, S.N. / Herr, A.B. / Lanka, E. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g6o.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g6o.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/1g6o ftp://data.pdbj.org/pub/pdb/validation_reports/g6/1g6o | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The functional hexamer can be generated from the two molecules in the asymmetric unit by three fold axes intrinsic to space group P6(3)22 |
-Components
#1: Protein | Mass: 37914.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: PWP4760 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: GenBank: 8843975, UniProt: Q7BK04*PLUS #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.6 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 1000, calcium acetate, glycerol, ADP-Mg, Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→500 Å / Num. all: 137723 / Num. obs: 27352 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.158 / % possible all: 71.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 137723 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 71.4 % / Mean I/σ(I) obs: 5.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 583702.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.381 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2 /
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.37 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.293 |