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- PDB-6dqq: Crystal structure of Haemophilus influenzae OppA complex with end... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dqq | ||||||
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Title | Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide | ||||||
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![]() | PEPTIDE BINDING PROTEIN / substrate-binding protein / ABC transporter | ||||||
Function / homology | ![]() peptide transmembrane transporter activity / peptide transport / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanaka, K.J. / Pinkett, H.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.4 KB | Display | ![]() |
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PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dqrC ![]() 6dqtC ![]() 6dquC ![]() 6dtfC ![]() 6dtgC ![]() 6dthC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: 86-028NP / Gene: oppA, NTHI1292 / Production host: ![]() ![]() | ||||
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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