[English] 日本語
Yorodumi- PDB-6dqr: Crystal structure of Haemophilus influenzae OppA complex with MGG -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dqr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Haemophilus influenzae OppA complex with MGG | ||||||
Components |
| ||||||
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: 2.08 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dqr.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dqr.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dqr_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dqr_full_validation.pdf.gz | 464.1 KB | Display | |
Data in XML | 6dqr_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 6dqr_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/6dqr ftp://data.pdbj.org/pub/pdb/validation_reports/dq/6dqr | HTTPS FTP |
-Related structure data
Related structure data | 6dqqC 6dqtC 6dquC 6dtfC 6dtgC 6dthC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||
---|---|---|---|---|---|
#2: Protein/peptide | Mass: 263.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae 86-028NP (bacteria) | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.49 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.6, 2.5M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.08→35.75 Å / Num. obs: 29098 / % possible obs: 99.1 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.08 / Net I/av σ(I): 15.6 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→35.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.717 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.197 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.79 Å2 / Biso mean: 48.405 Å2 / Biso min: 26.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→35.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|