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Yorodumi- PDB-2obm: Structural and biochemical analysis of a prototypical ATPase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2obm | ||||||
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Title | Structural and biochemical analysis of a prototypical ATPase from the type III secretion system of pathogenic bacteria | ||||||
Components | EscN | ||||||
Keywords | HYDROLASE / ATPase | ||||||
Function / homology | Function and homology information 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 ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O127:H6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Zarivach, R. / Vuckovic, M. / Deng, W. / Finlay, B.B. / Strynadka, N.C.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Structural analysis of a prototypical ATPase from the type III secretion system. Authors: Zarivach, R. / Vuckovic, M. / Deng, W. / Finlay, B.B. / Strynadka, N.C. | ||||||
History |
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Remark 600 | HETEROGEN AMP-PNP was used for crystallization setup which may be hydrolyzed to ADP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2obm.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2obm.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 2obm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2obm_validation.pdf.gz | 729.6 KB | Display | wwPDB validaton report |
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Full document | 2obm_full_validation.pdf.gz | 737.4 KB | Display | |
Data in XML | 2obm_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 2obm_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/2obm ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2obm | HTTPS FTP |
-Related structure data
Related structure data | 2oblC 1oblS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37667.402 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, residues 103-446 / Mutation: V393P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Species: Escherichia coli / Strain: E2348/69 / Gene: escN / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O52140, UniProt: B7UMA6*PLUS |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-ADP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 7% (w/v) PEG 8000, 0.1M Calcium Acetate, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5428 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5428 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 17405 / Num. obs: 17196 / % possible obs: 98.8 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 5.23 / Num. unique all: 1704 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OBL Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.517 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.775 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.247→2.305 Å / Total num. of bins used: 20
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