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- PDB-5j90: Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j90 | ||||||
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Title | Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae | ||||||
![]() | RagB/SusD domain protein | ||||||
![]() | Chitin-binding protein / Chitin-binding / SusD homolog / Bacteroidetes / Flavobacterium johnsoniae | ||||||
Function / homology | SusD-like / Susd and RagB outer membrane lipoprotein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / RagB/SusD domain protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Koropatkin, N.M. | ||||||
![]() | ![]() Title: A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Authors: Larsbrink, J. / Zhu, Y. / Kharade, S.S. / Kwiatkowski, K.J. / Eijsink, V.G. / Koropatkin, N.M. / McBride, M.J. / Pope, P.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.7 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 48.5 KB | Display | |
Data in CIF | ![]() | 77.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j5uC ![]() 4f7aS C: citing same article ( S: Starting model for refinement |
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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: 56582.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 150 mM Tris-HCl pH 8.5, 27% sokolan CP5. These crystals were briefly soaked in 10mM acetylchitopentaose prior to freezing with a solution of 20% ethylene glycol, 80% crystallization media Temp details: room temp |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen vapor | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.39→50 Å / Num. obs: 215603 / % possible obs: 99.2 % / Redundancy: 7.9 % / Biso Wilson estimate: 11.53 Å2 / Rmerge(I) obs: 0.056 / Net I/av σ(I): 44.733 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4F7A Resolution: 1.3932→36.574 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.9 Å2 / Biso mean: 15.7941 Å2 / Biso min: 5.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3932→36.574 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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