+Open data
-Basic information
Entry | Database: PDB / ID: 6hpa | ||||||
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Title | Crystal structure of a BA3943 mutant,a CE4 family pseudoenzyme | ||||||
Components | Putative polysaccharide deacetylase | ||||||
Keywords | UNKNOWN FUNCTION / Polysaccharide / Deacetylase / Peptidoglycan / Pseudoenzyme / Sporulation. | ||||||
Function / homology | Sporulation protein, polysaccharide deacetylase, YlxY / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / Putative polysaccharide deacetylase / Putative polysaccharide deacetylase Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å | ||||||
Authors | Molfetas, A. / Tomatsidou, N. / Kokkinidis, M. | ||||||
Funding support | Greece, 1items
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Citation | Journal: To Be Published Title: The resurrection of a dean enzyme Authors: Molfetas, A. / Tomatsidou, A. / Bouriotis, V. / Kokkinidis, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hpa.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hpa.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 6hpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hpa ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hpa | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31725.432 Da / Num. of mol.: 1 / Mutation: N94D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) Gene: ylxY, BA_3943, A9486_19545, BASH2_01993, CN272_11110, COL95_11150 Plasmid: pET26B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q4M7R6, UniProt: A0A6L7H2K2*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #4: 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: 2.09 Å3/Da / Density % sol: 41.19 % / Description: Cubic |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Ammonium Sulphate 2.8 M Tris Buffer PH=8 |
-Data collection
Diffraction | Mean temperature: 124 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07271 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016 |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07271 Å / Relative weight: 1 |
Reflection | Resolution: 1.554→78.883 Å / Num. obs: 38119 / % possible obs: 97.6 % / Redundancy: 12.538 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Χ2: 1.33 / Net I/av σ(I): 2.85 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.554→1.559 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4864 / CC1/2: 0.798 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BC1960 Resolution: 1.554→39.441 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.77 / 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: 1.554→39.441 Å
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Refine LS restraints |
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LS refinement shell |
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