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Yorodumi- PDB-2ffa: Crystal structure of ABC-ATPase H662A of the ABC-transporter HlyB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ffa | ||||||
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Title | Crystal structure of ABC-ATPase H662A of the ABC-transporter HlyB 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: 1.7 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 | 2ffa.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffa.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ffa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffa ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffa | HTTPS FTP |
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-Related structure data
Related structure data | 2ff7C 2ffbC 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
#1: Protein | Mass: 27685.781 Da / Num. of mol.: 1 / Fragment: amino acids 467-707 / Mutation: H662A 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: Chemical | ChemComp-MPD / ( |
#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: 2.13 Å3/Da / Density % sol: 42.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, 10% 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: Jan 13, 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: 1.7→20 Å / Num. obs: 24609 / % possible obs: 99.2 % / Observed criterion σ(F): 3.2 / Redundancy: 12.2 % / Rsym value: 0.062 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.163 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MT0 Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.619 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.059 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 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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