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Yorodumi- PDB-5xgx: Crystal structure of colwellia psychrerythraea strain 34H isoaspa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xgx | ||||||
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Title | Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with beta-isoaspartyl lysine | ||||||
Components | Isoaspartyl dipeptidase | ||||||
Keywords | HYDROLASE / Colwellia psychrerythraea / Isoaspartyl dipeptidase / IadA / beta-isoaspartyl lysine | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / beta-aspartyl-peptidase activity / metallopeptidase activity / proteolysis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Colwellia psychrerythraea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å | ||||||
Authors | Lee, J.H. / Lee, C.W. / Park, S.H. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H. Authors: Park, S.H. / Lee, C.W. / Lee, S.G. / Shin, S.C. / Kim, H.J. / Park, H. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xgx.cif.gz | 162.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xgx.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/5xgx ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xgx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42762.508 Da / Num. of mol.: 2 / Mutation: E80Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria) Strain: 34H / ATCC BAA-681 / Gene: iadA, CPS_1869 / Production host: Escherichia coli (E. coli) References: UniProt: Q484B6, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.64 Å3/Da / Density % sol: 53.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris propane pH 7.0 1 M ammonium citrate tribasic pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50.01 Å / Num. obs: 36407 / % possible obs: 97.1 % / Redundancy: 6.8 % / Net I/σ(I): 31.8 |
-Processing
Software |
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Refinement | Resolution: 2.33→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.989 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.708 Å2
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Refinement step | Cycle: 1 / Resolution: 2.33→50.01 Å
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