+Open data
-Basic information
Entry | Database: PDB / ID: 7czh | ||||||
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Title | PL24 ulvan lyase-Uly1 | ||||||
Components | Uly1 | ||||||
Keywords | LYASE / polysaccharide lyase / ulvan lyase / PL24 / beta-propeller | ||||||
Function / homology | F5/8 type C domain-containing protein Function and homology information | ||||||
Biological species | Catenovulum maritimum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 Å | ||||||
Authors | Zhang, Y.Z. / Chen, X.L. / Dong, F. / Xu, F. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2021 Title: Mechanistic Insights into Substrate Recognition and Catalysis of a New Ulvan Lyase of Polysaccharide Lyase Family 24. Authors: Xu, F. / Dong, F. / Sun, X.H. / Cao, H.Y. / Fu, H.H. / Li, C.Y. / Zhang, X.Y. / McMinn, A. / Zhang, Y.Z. / Wang, P. / Chen, X.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7czh.cif.gz | 228 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7czh.ent.gz | 177.4 KB | Display | PDB format |
PDBx/mmJSON format | 7czh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7czh_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 7czh_full_validation.pdf.gz | 450.2 KB | Display | |
Data in XML | 7czh_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 7czh_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/7czh ftp://data.pdbj.org/pub/pdb/validation_reports/cz/7czh | HTTPS FTP |
-Related structure data
-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: 55911.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Catenovulum maritimum (bacteria) / Gene: XM47_11230 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J8GWN9 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 200 mM calcium acetate hydrate (pH 6.5), 18% (w/v) polyethylene glycol (PEG) 8000, and 100 mM sodium cacodylate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.104→50 Å / Num. obs: 62242 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.219 / Rrim(I) all: 0.237 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.104→2.14 Å / Rmerge(I) obs: 0.337 / Num. unique obs: 3092 / Rrim(I) all: 0.365 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.104→47.496 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 20.93 / 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: 64.93 Å2 / Biso mean: 27.0946 Å2 / Biso min: 10.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.104→47.496 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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