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Yorodumi- PDB-1nlz: Crystal structure of unliganded traffic ATPase of the type IV sec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nlz | ||||||
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Title | Crystal structure of unliganded traffic ATPase of the type IV secretion system of helicobacter pylori | ||||||
Components | virB11 homolog | ||||||
Keywords | HYDROLASE / VirB11 ATPase / bacterial type IV secretion / HP0525 / helicobacter pylori | ||||||
Function / homology | Function and homology information secretion by the type IV secretion system / type IV secretion system complex / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å | ||||||
Authors | Savvides, S.N. / Yeo, H.J. / Beck, M.R. / Blaesing, F. / Lurz, R. / Lanka, E. / Buhrdorf, R. / Fischer, W. / Haas, R. / Waksman, G. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: VirB11 ATPases are dynamic hexameric assemblies: New insights into bacterial type IV secretion Authors: Savvides, S.N. / Yeo, H.J. / Beck, M.R. / Blaesing, F. / Lurz, R. / Lanka, E. / Buhrdorf, R. / Fischer, W. / Haas, R. / Waksman, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nlz.cif.gz | 354.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nlz.ent.gz | 301.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nlz_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
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Full document | 1nlz_full_validation.pdf.gz | 568.7 KB | Display | |
Data in XML | 1nlz_validation.xml.gz | 72.8 KB | Display | |
Data in CIF | 1nlz_validation.cif.gz | 98 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nlz ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nlz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37914.242 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HPO525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BK04 #2: 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: 2.62 Å3/Da / Density % sol: 52.71 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: PEG MME 2000, NaCl, Tris-HCl,glycerol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||
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-BM / Wavelength: 0.9793,0.9794,0.9667 | ||||||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→30 Å / Num. all: 74172 / Num. obs: 74172 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 3→3.1 Å / Rsym value: 0.382 / % possible all: 89 | ||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 89.4 % / Num. measured all: 291962 / Rmerge(I) obs: 0.083 | ||||||||||||
Reflection shell | *PLUS % possible obs: 88.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→29.7 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.719 Å2 / ksol: 0.322471 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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