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Yorodumi- PDB-6dqu: Crystal structure of Haemophilus influenzae OppA complex with GIINTL -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dqu | ||||||
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Title | Crystal structure of Haemophilus influenzae OppA complex with GIINTL | ||||||
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: 1.65 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 | 6dqu.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dqu.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/6dqu ftp://data.pdbj.org/pub/pdb/validation_reports/dq/6dqu | HTTPS FTP |
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-Related structure data
Related structure data | 6dqqC 6dqrC 6dqtC 6dtfC 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) / Strain (production host): BL21(DE3) / References: UniProt: Q4QLH0 |
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#2: Protein/peptide | Mass: 629.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae 86-028NP (bacteria) |
#3: Chemical | ChemComp-SO4 / |
#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: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.6, 2.1M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→35.88 Å / Num. obs: 58988 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3 / Num. unique obs: 2852 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→35.88 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.473 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.099 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: 90.68 Å2 / Biso mean: 31.322 Å2 / Biso min: 16.67 Å2
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Refinement step | Cycle: final / Resolution: 1.65→35.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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