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Yorodumi- PDB-2ffb: The crystal structure of the HlyB-NBD E631Q mutant in complex with ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ffb | ||||||
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Title | The crystal structure of the HlyB-NBD E631Q mutant in complex with ADP | ||||||
Components | Alpha-hemolysin translocation ATP-binding protein hlyB | ||||||
Keywords | TRANSPORT PROTEIN / ABC-transporter / ATPase | ||||||
Function / homology | Function and homology information protein secretion by the type I secretion system / type I protein secretion system complex / ATPase-coupled lipid transmembrane transporter activity / ABC-type transporter activity / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zaitseva, J. / Oswald, C. / Jumpertz, T. / Jenewein, S. / Holland, I.B. / Schmitt, L. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer. Authors: Zaitseva, J. / Oswald, C. / Jumpertz, T. / Jenewein, S. / Wiedenmann, A. / Holland, I.B. / Schmitt, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ffb.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffb.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ffb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffb ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffb | HTTPS FTP |
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-Related structure data
Related structure data | 2ff7C 2ffaC 2fgjC 2fgkC 1mt0S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27751.865 Da / Num. of mol.: 1 / Fragment: amino acids 467-707 / Mutation: E631Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hlyB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P08716 |
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#2: Chemical | ChemComp-ADP / |
#3: 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: 2.08 Å3/Da / Density % sol: 40.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, 16% PEG 6000, 5% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 8, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 16370 / % possible obs: 94.1 % / Observed criterion σ(F): 2.3 / Rsym value: 0.049 |
Reflection shell | Resolution: 1.9→1.95 Å / Mean I/σ(I) obs: 2.3 / Num. unique all: 16370 / Rsym value: 0.277 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1MT0 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.819 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R Free: 0.175 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.036 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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