+Open data
-Basic information
Entry | Database: PDB / ID: 6fpn | |||||||||
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Title | Lytic transglycosylase in action | |||||||||
Components | Putative soluble lytic murein 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: 1.44 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 | 6fpn.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fpn.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fpn_validation.pdf.gz | 412.9 KB | Display | wwPDB validaton report |
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Full document | 6fpn_full_validation.pdf.gz | 418.8 KB | Display | |
Data in XML | 6fpn_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6fpn_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/6fpn ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fpn | HTTPS FTP |
-Related structure data
Related structure data | 5o1jC 5o24C 5o29C 5o2nC 502nS C: citing same article (ref.) 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: 64768.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB1949 / Plasmid: PGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Gold / References: UniProt: Q9JXP1 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 2.35 Å3/Da / Density % sol: 47.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M 2% (v/v) PEG 400 0.1 M Hepes pH. 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→62.96 Å / Num. obs: 117919 / % possible obs: 97.42 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.16 |
Reflection shell | Resolution: 1.4→1.449 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 502N Resolution: 1.44→62.96 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.44→62.96 Å
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