+Open data
-Basic information
Entry | Database: PDB / ID: 5o29 | ||||||
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Title | Lytic transglycosylase in action | ||||||
Components | Transglycosylase | ||||||
Keywords | HYDROLASE / lytic transglycosylases / acid/base catalysis / peptidoglycan / bacteria | ||||||
Function / homology | Function and homology information catalytic activity / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3785 Å | ||||||
Authors | Williams, A.H. / Hoauz, A. / Boneca, I.G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: A step-by-stepin crystalloguide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase. Authors: Williams, A.H. / Wheeler, R. / Rateau, L. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Taha, M.K. / Boneca, I.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o29.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o29.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o29_validation.pdf.gz | 420.2 KB | Display | wwPDB validaton report |
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Full document | 5o29_full_validation.pdf.gz | 423.4 KB | Display | |
Data in XML | 5o29_validation.xml.gz | 29 KB | Display | |
Data in CIF | 5o29_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/5o29 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/5o29 | HTTPS FTP |
-Related structure data
Related structure data | 5o1jC 5o24C 5o2nC 6fpnC 4yim 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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Unit cell |
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-Components
#1: Protein | Mass: 65684.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: slt, ERS514729_01258 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): gold References: UniProt: A0A0Y5YPU4, UniProt: Q9JXP1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % / Description: Rod Shape |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 33% (w/v) PEG 6000, Hepes pH 7.5 or 3) 0.2M Zinc acetate, or 0.1 M Sodium cacodylate pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3785→45.93 Å / Num. obs: 119443 / % possible obs: 93.76 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1431 / Rpim(I) all: 0.06957 / Net I/σ(I): 10.73 |
Reflection shell | Resolution: 1.379→1.428 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 11548 / Rpim(I) all: 0.1 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YIM 4yim Resolution: 1.3785→45.93 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3785→45.93 Å
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Refine LS restraints |
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LS refinement shell |
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