+Open data
-Basic information
Entry | Database: PDB / ID: 4k9s | ||||||
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Title | Peptidoglycan O-acetylesterase in action, setmet | ||||||
Components | GDSL-like Lipase/Acylhydrolase family protein | ||||||
Keywords | HYDROLASE / Alpha/Beta Fold / Peptidoglycan hydrolase | ||||||
Function / homology | Jelly Rolls - #1360 / SGNH hydrolase / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / : Function and homology information | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.334 Å | ||||||
Authors | Williams, A.H. / Gompert Boneca, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members. Authors: Williams, A.H. / Veyrier, F.J. / Bonis, M. / Michaud, Y. / Raynal, B. / Taha, M.K. / White, S.W. / Haouz, A. / 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 | 4k9s.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k9s.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 4k9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/4k9s ftp://data.pdbj.org/pub/pdb/validation_reports/k9/4k9s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41306.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: Neisseria meningitidis, NM4119_1198 / Plasmid: PGEX 4TI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: L5SU74 #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: 2.14 Å3/Da / Density % sol: 42.53 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Hepes pH 7.5 10-40% Peg 10000 , VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.334→40.41 Å / Num. obs: 2673 / % possible obs: 88.48 % / Observed criterion σ(F): 2.51 / Observed criterion σ(I): 2.51 |
Reflection shell | Resolution: 2.334→2.417 Å / % possible all: 98.13 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.334→40.41 Å / SU ML: 0.32 / σ(F): 1.39 / Phase error: 24.5 / 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: 2.334→40.41 Å
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Refine LS restraints |
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LS refinement shell |
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