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Yorodumi- PDB-4ly4: Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ly4 | ||||||
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Title | Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori | ||||||
Components | peptidoglycan deacetylase | ||||||
Keywords | HYDROLASE / metallo enzyme / peptidoglycan / TIM barrel / deacetylase / Peptidoglycan Deacetylase | ||||||
Function / homology | Function and homology information acetylxylan esterase / acetylxylan esterase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / xylan catabolic process / cell wall organization / metal ion binding Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å | ||||||
Authors | Shaik, M.M. / Zanotti, G. | ||||||
Citation | Journal: Proteins / Year: 2014 Title: Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations. Authors: Shaik, M.M. / Bhattacharjee, N. / Bhattacharjee, A. / Field, M.J. / Zanotti, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ly4.cif.gz | 247.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ly4.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ly4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ly4_validation.pdf.gz | 463.9 KB | Display | wwPDB validaton report |
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Full document | 4ly4_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 4ly4_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 4ly4_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4ly4 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4ly4 | HTTPS FTP |
-Related structure data
Related structure data | 3qbuS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37566.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: HP0310, HPG27_289 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5ZA76 #2: Chemical | ChemComp-ZN / #3: 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: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M Ammonium Sulphate, 0.1M Tri Sodium citrate pH 5.6, 15% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.2821 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 8, 2011 / Details: double crystal monochromator |
Radiation | Monochromator: double crystal monochromator, Crystal type Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2821 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→31.85 Å / Num. all: 68530 / Num. obs: 68530 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 2.5 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QBU Resolution: 2.199→30.475 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 20.1 / 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: 2.199→30.475 Å
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Refine LS restraints |
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LS refinement shell |
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