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Yorodumi- PDB-6dtf: Crystal structure of Haemophilus influenzae OppA complex with KKK -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dtf | ||||||
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Title | Crystal structure of Haemophilus influenzae OppA complex with KKK | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / substrate-binding protein / ABC transporter | ||||||
Function / homology | Function and homology information ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) Haemophilus influenzae 86-028NP (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Tanaka, K.J. / Pinkett, H.W. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2019 Title: Oligopeptide-binding protein from nontypeableHaemophilus influenzaehas ligand-specific sites to accommodate peptides and heme in the binding pocket. Authors: Tanaka, K.J. / Pinkett, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dtf.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dtf.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 6dtf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/6dtf ftp://data.pdbj.org/pub/pdb/validation_reports/dt/6dtf | HTTPS FTP |
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-Related structure data
Related structure data | 6dqqC 6dqrC 6dqtC 6dquC 6dtgC 6dthC 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: 59987.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria) Strain: 86-028NP / Gene: oppA, NTHI1292 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QLH0 | ||
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#2: Protein/peptide | Mass: 405.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae 86-028NP (bacteria) | ||
#3: Chemical | #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: 1.98 Å3/Da / Density % sol: 37.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.6, 2.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.73 Å / Num. obs: 48105 / % possible obs: 97.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.7 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.73 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.236 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123 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: 104.84 Å2 / Biso mean: 40.6 Å2 / Biso min: 25.39 Å2
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Refinement step | Cycle: final / Resolution: 1.75→46.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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