+Open data
-Basic information
Entry | Database: PDB / ID: 8qx6 | ||||||
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Title | Novel laminarin-binding CBM X584 | ||||||
Components | PKD domain-containing protein | ||||||
Keywords | SUGAR BINDING PROTEIN / CBM X584 / Surface glycan binding protein / carbohydrate binding module / ligand complex | ||||||
Function / homology | Polycystic kidney disease (PKD) domain profile. / PKD domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / PKD domain-containing protein Function and homology information | ||||||
Biological species | Christiangramia forsetii KT0803 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zuehlke, M.K. / Jeudy, A. / Czjzek, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Environ.Microbiol. / Year: 2024 Title: Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms. Authors: Zuhlke, M.K. / Ficko-Blean, E. / Bartosik, D. / Terrapon, N. / Jeudy, A. / Jam, M. / Wang, F. / Welsch, N. / Durwald, A. / Martin, L.T. / Larocque, R. / Jouanneau, D. / Eisenack, T. / ...Authors: Zuhlke, M.K. / Ficko-Blean, E. / Bartosik, D. / Terrapon, N. / Jeudy, A. / Jam, M. / Wang, F. / Welsch, N. / Durwald, A. / Martin, L.T. / Larocque, R. / Jouanneau, D. / Eisenack, T. / Thomas, F. / Trautwein-Schult, A. / Teeling, H. / Becher, D. / Schweder, T. / Czjzek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qx6.cif.gz | 127.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qx6.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qx6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8qx6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8qx6_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 8qx6_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/8qx6 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/8qx6 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18092.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: isolated carbohydrate binding module part of the protein with Uniprot code A0M709 Source: (gene. exp.) Christiangramia forsetii KT0803 (bacteria) Gene: GFO_3465 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0M709 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 292 K / Method: counter-diffusion / pH: 7 Details: 2.5 M ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0, 6% ethanol and 4% polyethylenglycol (PEG) 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 gasstream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.42 Å / Num. obs: 23977 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.81 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1610 / CC1/2: 0.58 / Rpim(I) all: 0.59 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.42 Å / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.186
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Displacement parameters | Biso mean: 32.27 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→47.42 Å
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Refine LS restraints | Type: NCS Local / Dev ideal: 0.14 / Weight: 0.05 | ||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.95 Å
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