[English] 日本語
Yorodumi- PDB-8c5n: Sub-atomic resolution structure of the chitin-binding protein D (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5n | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Sub-atomic resolution structure of the chitin-binding protein D (CbpD) from Pseudomonas aeruginosa | ||||||||||||
Components | Chitin-binding protein CbpD | ||||||||||||
Keywords | OXIDOREDUCTASE / monooxygenase / LPMO / chitin-binding / histidine brace motif / polysaccharide / Pseudomonas aeruginosa / apo enzyme | ||||||||||||
Function / homology | N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / chitin binding / Immunoglobulin E-set / extracellular region / Chitin-binding protein CbpD Function and homology information | ||||||||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.75 Å | ||||||||||||
Authors | Cordara, G. / Krengel, U. / Golten, O. / Vaaje-Kolstad, G. / Vinther Soerensen, H. | ||||||||||||
Funding support | Norway, 3items
| ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Immunization with lytic polysaccharide monooxygenase CbpD induces protective immunity against Pseudomonas aeruginosa pneumonia. Authors: Askarian, F. / Tsai, C.M. / Cordara, G. / Zurich, R.H. / Bjanes, E. / Golten, O. / Vinther Sorensen, H. / Kousha, A. / Meier, A. / Chikwati, E. / Bruun, J.A. / Ludviksen, J.A. / Choudhury, B. ...Authors: Askarian, F. / Tsai, C.M. / Cordara, G. / Zurich, R.H. / Bjanes, E. / Golten, O. / Vinther Sorensen, H. / Kousha, A. / Meier, A. / Chikwati, E. / Bruun, J.A. / Ludviksen, J.A. / Choudhury, B. / Trieu, D. / Davis, S. / Edvardsen, P.K.T. / Mollnes, T.E. / Liu, G.Y. / Krengel, U. / Conrad, D.J. / Vaaje-Kolstad, G. / Nizet, V. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8c5n.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8c5n.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5n ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5n | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20937.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Strain: UCBPP-PA14 / Gene: cpbD, PA14_53250 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): K12 / Variant (production host): BL21 (DE3) / References: UniProt: Q02I11 |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.9 % / Description: large prism |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 150 mM NaCl, 15 mM Tris-HCl pH 7.5, 0.2 M ammonium chloride, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.65255 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2020 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM) |
Radiation | Monochromator: At 26 m, Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.65255 Å / Relative weight: 1 |
Reflection | Resolution: 0.75→47.4 Å / Num. obs: 198464 / % possible obs: 97 % / Redundancy: 19.9 % / Biso Wilson estimate: 6.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.012 / Rrim(I) all: 0.056 / Χ2: 0.98 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 0.75→0.76 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7613 / CC1/2: 0.3 / Χ2: 0.73 / % possible all: 76 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.75→47.357 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.253 / SU ML: 0.008 / Cross valid method: FREE R-VALUE / ESU R: 0.012 / ESU R Free: 0.012 Details: Hydrogens have been used if present in the input file
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.591 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.75→47.357 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|