+Open data
-Basic information
Entry | Database: PDB / ID: 5gkq | |||||||||
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Title | Structure of PL6 family alginate lyase AlyGC mutant-R241A | |||||||||
Components | AlyGC mutant - R241A | |||||||||
Keywords | LYASE / Alginate lyase / PL6 | |||||||||
Function / homology | PL-6 family / Chondroitinase B / Pectin lyase fold / Pectin lyase fold/virulence factor / metal ion binding / AlyGC mutant - R241A Function and homology information | |||||||||
Biological species | Glaciecola chathamensis S18K6 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.565 Å | |||||||||
Authors | Zhang, Y.Z. / Wang, P. / Xu, F. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6 Authors: Xu, F. / Dong, F. / Wang, P. / Cao, H.Y. / Li, C.Y. / Li, P.Y. / Pang, X.H. / Zhang, Y.Z. / 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 | 5gkq.cif.gz | 296.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gkq.ent.gz | 237.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gkq_validation.pdf.gz | 726.2 KB | Display | wwPDB validaton report |
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Full document | 5gkq_full_validation.pdf.gz | 751.2 KB | Display | |
Data in XML | 5gkq_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 5gkq_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gkq ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gkq | HTTPS FTP |
-Related structure data
Related structure data | 5gkdSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 80289.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glaciecola chathamensis S18K6 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4NYD8*PLUS #2: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-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: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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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: 3.09 Å3/Da / Density % sol: 60.16 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100mM HEPES-NaOH (pH 7.3), 8% ethylene glycol, 11% polyethylene glycol (PEG) 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.565→47.8 Å / Num. obs: 61999 / % possible obs: 96 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.565→2.657 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GKD Resolution: 2.565→47.8 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.67 / 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: 2.565→47.8 Å
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Refine LS restraints |
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LS refinement shell |
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