[English] 日本語
Yorodumi- PDB-6dtg: Crystal structure of Haemophilus influenzae OppA complex with YLG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dtg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Haemophilus influenzae OppA complex with YLGANGRGGGS | ||||||
Components |
| ||||||
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) Haemophilus influenzae 86-028NP (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6dtg.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dtg.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dtg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dtg_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dtg_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | 6dtg_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 6dtg_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/6dtg ftp://data.pdbj.org/pub/pdb/validation_reports/dt/6dtg | HTTPS FTP |
-Related structure data
Related structure data | 6dqqC 6dqrC 6dqtC 6dquC 6dtfC 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: 593.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus influenzae 86-028NP (bacteria) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.81 % |
---|---|
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: 1.0782 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: 1.9→46.66 Å / Num. obs: 39899 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 9 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.66 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.048 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.138 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: 97.36 Å2 / Biso mean: 33.857 Å2 / Biso min: 20.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→46.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|