+Open data
-Basic information
Entry | Database: PDB / ID: 6h5f | |||||||||
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Title | LtgA disordered Helix | |||||||||
Components | Putative soluble lytic murein transglycosylase | |||||||||
Keywords | TRANSFERASE / Peptidoglycan / antibiotic resistance / enzyme hub | |||||||||
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 NM422 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Williams, A.H. | |||||||||
Citation | Journal: Elife / Year: 2020 Title: Defective lytic transglycosylase disrupts cell morphogenesis by hindering cell wall de-O-acetylation inNeisseria meningitidis. Authors: Williams, A.H. / Wheeler, R. / Deghmane, A.E. / Santecchia, I. / Schaub, R.E. / Hicham, S. / Moya Nilges, M. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Dillard, J.P. / Robins, W.P. / ...Authors: Williams, A.H. / Wheeler, R. / Deghmane, A.E. / Santecchia, I. / Schaub, R.E. / Hicham, S. / Moya Nilges, M. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Dillard, J.P. / Robins, W.P. / Taha, M.K. / Gomperts Boneca, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h5f.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h5f.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 6h5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h5f_validation.pdf.gz | 406.1 KB | Display | wwPDB validaton report |
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Full document | 6h5f_full_validation.pdf.gz | 409.7 KB | Display | |
Data in XML | 6h5f_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6h5f_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h5f ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h5f | HTTPS FTP |
-Related structure data
Related structure data | 4yib 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: 67824.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis NM422 (bacteria) Gene: NMB1949 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q9JXP1 |
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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: 2.17 Å3/Da / Density % sol: 43.38 % / Description: RECTANGULAR IN SHAPE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 33% (W/V) PEG 6000, 0.01 M TRI SODIUM CITRATE., PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.955→49.06 Å / Num. obs: 40499 / % possible obs: 98.6 % / Redundancy: 7.74 % / Rsym value: 0.055 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 1.47 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YIB 4yib Resolution: 2→49.06 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.06 Å
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Refine LS restraints |
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LS refinement shell |
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