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- PDB-7o78: Structure of the PL6 family chondroitinase B from Pseudopedobacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o78 | ||||||
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Title | Structure of the PL6 family chondroitinase B from Pseudopedobacter saltans, Pedsa3807 | ||||||
![]() | Polysaccharide lyase from Pseudopedobacter saltans, Pedsa3807 | ||||||
![]() | LYASE / beta helix | ||||||
Function / homology | PL-6 family / Chondroitinase B / Pectin lyase fold / Pectin lyase fold/virulence factor / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ballut, L. / Violot, S. / Carrique, L. / Aghajari, N. | ||||||
![]() | ![]() Title: Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity. Authors: Violot, S. / Galisson, F. / Carrique, L. / Jugnarain, V. / Conchou, L. / Robert, X. / Thureau, A. / Helbert, W. / Aghajari, N. / Ballut, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.9 KB | Display | ![]() |
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PDB format | ![]() | 172.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.4 KB | Display | ![]() |
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Full document | ![]() | 425.5 KB | Display | |
Data in XML | ![]() | 42.4 KB | Display | |
Data in CIF | ![]() | 66 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o77C ![]() 7o79C ![]() 7o7aC ![]() 7o7tC ![]() 7o84C ![]() 1ofmS S: Starting model for refinement C: citing same article ( |
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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: 55481.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643 Gene: Pedsa_3807 / Plasmid: pET28a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M tri-Li citrate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→75.36 Å / Num. obs: 135111 / % possible obs: 96 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.58→1.62 Å / Num. unique obs: 10276 / CC1/2: 0.844 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OFM Resolution: 1.58→58.35 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.88 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.81 Å2 / Biso mean: 24.5804 Å2 / Biso min: 12.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.58→58.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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