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Yorodumi- PDB-8dqm: Crystal structure of isoaspartyl aminopeptidase from Roseivivax h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dqm | ||||||
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Title | Crystal structure of isoaspartyl aminopeptidase from Roseivivax halodurans DSM 15395 | ||||||
Components | (Isoaspartyl aminopeptidase) x 2 | ||||||
Keywords | HYDROLASE / IaaA | ||||||
Function / homology | Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal / hydrolase activity / Asparaginase Function and homology information | ||||||
Biological species | Roseivivax halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sharon, I. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Sci Rep / Year: 2023 Title: Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation. Authors: Sharon, I. / Schmeing, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dqm.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dqm.ent.gz | 177.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqm ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqm | HTTPS FTP |
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-Related structure data
Related structure data | 8dqnC C: citing same article (ref.) |
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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: 18660.852 Da / Num. of mol.: 4 / Fragment: N-terminal residues 1-177 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseivivax halodurans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X7EBZ8 #2: Protein | Mass: 14271.830 Da / Num. of mol.: 4 / Fragment: C-terminal residues 178-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Roseivivax halodurans (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: X7EBZ8 #3: Chemical | ChemComp-NA / #4: 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: 3.91 Å3/Da / Density % sol: 68.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M bis-tris propane pH 8.5, 0.2 M disodium malonate and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.522 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.522 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→98.96 Å / Num. obs: 59664 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.76 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 5893 / CC1/2: 0.953 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold model Resolution: 2.7→98.96 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 26.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→98.96 Å
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Refine LS restraints |
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LS refinement shell |
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