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Yorodumi- PDB-6dqq: Crystal structure of Haemophilus influenzae OppA complex with end... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dqq | ||||||
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Title | Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / substrate-binding protein / ABC transporter | ||||||
Function / homology | Function and homology information peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 6dqq.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dqq.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 6dqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dqq_validation.pdf.gz | 456.4 KB | Display | wwPDB validaton report |
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Full document | 6dqq_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 6dqq_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 6dqq_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/6dqq ftp://data.pdbj.org/pub/pdb/validation_reports/dq/6dqq | HTTPS FTP |
-Related structure data
Related structure data | 6dqrC 6dqtC 6dquC 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: 58784.629 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: 302.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.09 Å3/Da / Density % sol: 41.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate pH 4.6 and 2.4M 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: Jun 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0782 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→46.67 Å / Num. obs: 42868 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Net I/σ(I): 18.6 / Num. measured all: 572217 / Scaling rejects: 13 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.556 / Num. unique obs: 2595 / CC1/2: 0.972 / Rpim(I) all: 0.154 / Rrim(I) all: 0.577 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.67 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.277 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128 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: 94.13 Å2 / Biso mean: 32.37 Å2 / Biso min: 19 Å2
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Refinement step | Cycle: final / Resolution: 1.85→46.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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