+Open data
-Basic information
Entry | Database: PDB / ID: 7w13 | ||||||
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Title | Complex structure of alginate lyase PyAly with M8 | ||||||
Components | Alginate lyase | ||||||
Keywords | LYASE / PL7 family / alginate lyase / complex | ||||||
Function / homology | Alginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase Function and homology information | ||||||
Biological species | Neopyropia yezoensis (susabi-nori) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Liu, W.Z. / Lyu, Q.Q. / Li, Z.J. / Zhang, K.K. | ||||||
Funding support | China, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements. Authors: Zhang, K. / Li, Z. / Zhu, Q. / Cao, H. / He, X. / Zhang, X.H. / Liu, W. / Lyu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w13.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w13.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 7w13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w13_validation.pdf.gz | 727.7 KB | Display | wwPDB validaton report |
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Full document | 7w13_full_validation.pdf.gz | 729.2 KB | Display | |
Data in XML | 7w13_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 7w13_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/7w13 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/7w13 | HTTPS FTP |
-Related structure data
Related structure data | 7w12C 7w16C 7w18C 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: 27055.221 Da / Num. of mol.: 1 / Mutation: H125A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neopyropia yezoensis (susabi-nori) / Gene: PyAly / Production host: Escherichia coli (E. coli) / References: UniProt: D2KX85 |
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#2: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: 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: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: Imidazole, Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 29611 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rsym value: 0.077 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.62→1.65 Å / Num. unique obs: 1467 / Rsym value: 0.077 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→39.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 1.899 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.09 Å2 / Biso mean: 14.153 Å2 / Biso min: 6.66 Å2
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Refinement step | Cycle: final / Resolution: 1.65→39.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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