+Open data
-Basic information
Entry | Database: PDB / ID: 7w2a | ||||||
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Title | gliadinase Bga1903 | ||||||
Components | PeptidaseProtease | ||||||
Keywords | LYASE / Serine Protease / Celiac Disease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia gladioli pv. gladioli (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Meng, M. | ||||||
Funding support | 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Crystal structure of a Burkholderia peptidase and modification of the substrate-binding site for enhanced hydrolytic activity toward gluten-derived pro-immunogenic peptides. Authors: Liu, Y.Y. / Lin, I.C. / Chen, P.C. / Lee, C.C. / Meng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w2a.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w2a.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 7w2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/7w2a ftp://data.pdbj.org/pub/pdb/validation_reports/w2/7w2a | HTTPS FTP |
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-Related structure data
Related structure data | 5yl7S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 36205.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Burkholderia gladioli pv. gladioli (bacteria) References: UniProt: A0A808VY57 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3 Å3/Da / Density % sol: 59.05 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 14.4% (V/V) PEG8000, 80 mM C2H6AsNaO2/HCl (PH6.5), 160 mM Calcium acetate, 20% (V/V) Glycerol |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 24, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→30 Å / Num. obs: 111122 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.042 / Rrim(I) all: 0.099 / Χ2: 1.035 / Net I/σ(I): 10.4 / Num. measured all: 620583 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5yl7 Resolution: 1.6→26.6 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 16.08 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.16 Å2 / Biso mean: 15.5927 Å2 / Biso min: 4.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→26.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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