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Yorodumi- PDB-6pu3: ABC transporter-associated periplasmic binding protein DppA from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pu3 | ||||||
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Title | ABC transporter-associated periplasmic binding protein DppA from Helicobacter pylori | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / DppA / type II / periplasmic binding protein / Periplasmic peptide binding protein | ||||||
Function / homology | Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / ATP-binding cassette (ABC) transporter complex / transmembrane transport / Heme-binding protein A Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Rahman, M.M. / Machuca, M.A. / Khan, M.F. / Barlow, C.K. / Schittenhelm, R.B. / Roujeinikova, A. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2019 Title: Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori. Authors: Rahman, M.M. / Machuca, M.A. / Khan, M.F. / Barlow, C.K. / Schittenhelm, R.B. / Roujeinikova, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pu3.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pu3.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 6pu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pu3_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 6pu3_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 6pu3_validation.xml.gz | 27.3 KB | Display | |
Data in CIF | 6pu3_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/6pu3 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/6pu3 | HTTPS FTP |
-Related structure data
Related structure data | 6ofqC 5f1qS 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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2 |
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Unit cell |
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Details | The author determined assembly is a monomer. The tetrapeptide, Chain B, has co-purified with the protein and is not a part of the biological assembly |
-Components
#1: Protein | Mass: 60510.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: hbpA, HPPMSS1_c01141 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q9Y393 |
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#2: Protein/peptide | Mass: 364.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Probably co-purified with the protein / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
#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: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23% w/v polyethylene glycol (PEG) 3350, 0.25 M tri-ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.12 Å / Num. obs: 59276 / % possible obs: 99 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.348 / Num. unique obs: 3464 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F1Q Resolution: 1.8→46.12 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.21 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.22 Å2 / Biso mean: 13.636 Å2 / Biso min: 3.71 Å2
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Refinement step | Cycle: final / Resolution: 1.8→46.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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