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Yorodumi- PDB-5gt5: Structural basis of the specific activity and thermostability of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gt5 | ||||||
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Title | Structural basis of the specific activity and thermostability of pectate lyase (pelN) from Paenibacillus sp. 0602 | ||||||
Components | Pectate lyase | ||||||
Keywords | LYASE / pectate lyase / Paenibacillus sp. 0602 | ||||||
Function / homology | Pectate lyase / Pectate lyase / Amb_all / pectate lyase / pectate lyase activity / Pectin lyase fold/virulence factor / polysaccharide catabolic process / extracellular region / Pectate lyase Function and homology information | ||||||
Biological species | Paenibacillus sp. 0602 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å | ||||||
Authors | Zhou, Z.P. / Liu, Y. / Song, J.N. | ||||||
Funding support | China, 1items
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Citation | Journal: Appl. Microbiol. Biotechnol. / Year: 2017 Title: Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming. Authors: Zhou, Z. / Liu, Y. / Chang, Z. / Wang, H. / Leier, A. / Marquez-Lago, T.T. / Ma, Y. / Li, J. / Song, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gt5.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gt5.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gt5_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 5gt5_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 5gt5_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 5gt5_validation.cif.gz | 74.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/5gt5 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/5gt5 | HTTPS FTP |
-Related structure data
Related structure data | 3zscS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48273.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. 0602 (bacteria) / Gene: pelN / Production host: Escherichia coli (E. coli) / References: UniProt: W8CR80, pectate lyase #2: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 3000, 100mM Na2HPO4 / PH range: 4.0-4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: May 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 629583 / % possible obs: 99.8 % / Redundancy: 7.4 % / Net I/σ(I): 14.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZSC Resolution: 1.449→34.431 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 17.14 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.449→34.431 Å
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Refine LS restraints |
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LS refinement shell |
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