+Open data
-Basic information
Entry | Database: PDB / ID: 7drq | ||||||
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Title | Crystal structure of polysaccharide lyase Uly1 | ||||||
Components | Uly1 | ||||||
Keywords | LYASE / ulvan lyase / polysaccharide lyase family 24 / marine bacterium | ||||||
Function / homology | BNR repeat-containing family member / metal ion binding / Uncharacterized protein Function and homology information | ||||||
Biological species | Catenovulum maritimum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å | ||||||
Authors | Chen, X.L. / Cao, H.Y. / Xu, F. / Dong, 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 | 7drq.cif.gz | 232.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7drq.ent.gz | 189.4 KB | Display | PDB format |
PDBx/mmJSON format | 7drq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7drq_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 7drq_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 7drq_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 7drq_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/7drq ftp://data.pdbj.org/pub/pdb/validation_reports/dr/7drq | 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: 57404.820 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 (E. coli) / References: UniProt: A0A0J8GWN9 #2: Chemical | ChemComp-CA / #3: 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: 2.52 Å3/Da / Density % sol: 51.14 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 200 mM calcium acetate, 100 mM MES (pH 6.0), 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 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: 1.79→37.11 Å / Num. obs: 101227 / % possible obs: 99.16 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Net I/σ(I): 22.79 |
Reflection shell | Resolution: 1.79→1.86 Å / Redundancy: 7 % / Rmerge(I) obs: 0.286 / Num. unique obs: 9595 / Rpim(I) all: 0.116 / Rrim(I) all: 0.309 / % possible all: 94.48 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→37.11 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.4 / 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: 54.05 Å2 / Biso mean: 19.1079 Å2 / Biso min: 4.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→37.11 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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