+Open data
-Basic information
Entry | Database: PDB / ID: 8khv | |||||||||
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Title | The crystal structure of glycosaminoglycan lyase GAGase II | |||||||||
Components | Heparinase II/III-like protein | |||||||||
Keywords | LYASE / Glycosaminoglycan / PL_35 | |||||||||
Function / homology | Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / lyase activity / : / Heparinase II/III-like protein Function and homology information | |||||||||
Biological species | Spirosoma fluviale (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | |||||||||
Authors | Wei, L. / Cao, H.Y. / Li, F.C. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: The crystal structure of glycosaminoglycan lyase GAGase VII Authors: Wei, L. / Cao, H.Y. / Li, F.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8khv.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8khv.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 8khv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8khv_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 8khv_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 8khv_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 8khv_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/8khv ftp://data.pdbj.org/pub/pdb/validation_reports/kh/8khv | HTTPS FTP |
-Related structure data
Related structure data | 8khwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68455.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spirosoma fluviale (bacteria) / Gene: SAMN06269250_2316 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A286FIB6 | ||||
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#2: Chemical | ChemComp-MN / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES (pH 7.0), 12% (w/v) polyethylene glycol (PEG) 6000 and 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.01 Å / Num. obs: 86421 / % possible obs: 98.55 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4092 / CC1/2: 0.964 / Rpim(I) all: 0.1 / Rrim(I) all: 0.23 / % possible all: 92.04 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→44.01 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.48 / 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: 48.81 Å2 / Biso mean: 13.383 Å2 / Biso min: 1.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→44.01 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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