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Yorodumi- PDB-6ljl: Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ljl | |||||||||
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Title | Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate | |||||||||
Components | Heparinase II/III-like protein | |||||||||
Keywords | LYASE / Heparin / Heparan sulfate / heparinase / crystall | |||||||||
Function / homology | Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / lyase activity / Immunoglobulin-like fold / Heparinase II/III-like protein Function and homology information | |||||||||
Biological species | Bacteroides intestinalis DSM 17393 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | |||||||||
Authors | Zhang, Q.D. / Cao, H.Y. / Wei, L. / Li, F.C. / Zhang, Y.Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Discovery of exolytic heparinases and their catalytic mechanism and potential application. Authors: Zhang, Q. / Cao, H.Y. / Wei, L. / Lu, D. / Du, M. / Yuan, M. / Shi, D. / Chen, X. / Wang, P. / Chen, X.L. / Chi, L. / Zhang, Y.Z. / Li, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ljl.cif.gz | 205 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ljl.ent.gz | 156.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ljl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ljl_validation.pdf.gz | 914.9 KB | Display | wwPDB validaton report |
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Full document | 6ljl_full_validation.pdf.gz | 921.9 KB | Display | |
Data in XML | 6ljl_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 6ljl_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6ljl ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6ljl | HTTPS FTP |
-Related structure data
Related structure data | 6ljaSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 99898.297 Da / Num. of mol.: 1 / Mutation: Y390A,H555A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides intestinalis DSM 17393 (bacteria) Gene: BACINT_00178 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3C5J6 | ||||
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#2: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D- ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 23% PEG 1500, 100mM MMT (DL-malic acid, MES, and Tris), pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→82.86 Å / Num. obs: 72171 / % possible obs: 82.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Net I/σ(I): 22.23 |
Reflection shell | Resolution: 1.73→1.83 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 7702 / CC1/2: 0.933 / Rpim(I) all: 0.149 / Rrim(I) all: 0.363 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LJA Resolution: 1.73→82.86 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.56 / Stereochemistry target values: ML
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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: 104.74 Å2 / Biso mean: 25.327 Å2 / Biso min: 13.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.73→82.86 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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