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Yorodumi- PDB-7fhu: Crystal structure of Multi-functional Polysaccharide lyase Smlt14... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fhu | |||||||||
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Title | Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 8.5 | |||||||||
Components | Polysaccharide lyase | |||||||||
Keywords | LYASE / Anionic Polysaccharide lyase | |||||||||
Function / homology | Function and homology information glucuronan lyase / glucuronan lyase activity / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / hyaluronate lyase / hyaluronate lyase activity / polysaccharide catabolic process / cell outer membrane / periplasmic space Similarity search - Function | |||||||||
Biological species | Stenotrophomonas maltophilia K279a (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | |||||||||
Authors | Pandey, S. / Berger, B.W. / Acharya, R. | |||||||||
Funding support | India, United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural insights into the mechanism of pH-selective substrate specificity of the polysaccharide lyase Smlt1473. Authors: Pandey, S. / Mahanta, P. / Berger, B.W. / Acharya, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fhu.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fhu.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 7fhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fhu_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 7fhu_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 7fhu_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 7fhu_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/7fhu ftp://data.pdbj.org/pub/pdb/validation_reports/fh/7fhu | HTTPS FTP |
-Related structure data
Related structure data | 7fhvC 7fhwC 7fhxC 7fhyC 7fhzC 7fi0C 7fi1C 7fi2C 1qazS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35428.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia K279a (bacteria) Strain: K279a / Gene: Smlt1473 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: B2FHL8, Lyases; Carbon-oxygen lyases; Acting on polysaccharides #2: Chemical | ChemComp-SO4 / #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: 2.17 Å3/Da / Density % sol: 42.76 % Description: Long rod-shaped THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M lithium sulfate monohydrate, 0.1M Tris-HCl pH-8.5, 30% (w/v) PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 26, 2016 / Details: HELIOS-MX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→43.89 Å / Num. obs: 22678 / % possible obs: 100 % / Redundancy: 17.66 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1232 / Net I/σ(I): 19.97 |
Reflection shell | Resolution: 2.43→2.53 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.4421 / Mean I/σ(I) obs: 5.11 / Num. unique obs: 2531 / CC1/2: 0.948 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QAZ Resolution: 2.43→43.854 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.186 / SU B: 10.567 / SU ML: 0.24 / Average fsc free: 0.8887 / Average fsc work: 0.9159 / Cross valid method: FREE R-VALUE / ESU R: 1.026 / ESU R Free: 0.327 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.892 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→43.854 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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