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Yorodumi- PDB-6ah8: Marine bacterial prolidase with promiscuous organophosphorus hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ah8 | ||||||
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Title | Marine bacterial prolidase with promiscuous organophosphorus hydrolase activity | ||||||
Components | Xaa-Pro dipeptidase | ||||||
Keywords | HYDROLASE / prolidase / promiscuous phosphotriesterase | ||||||
Function / homology | Function and homology information phosphoric triester hydrolase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / metalloexopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudoalteromonas lipolytica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Jian, Y. | ||||||
Citation | Journal: Biotechnol.Bioeng. / Year: 2020 Title: Repurposing a bacterial prolidase for organophosphorus hydrolysis: Reshaped catalytic cavity switches substrate selectivity. Authors: Yang, J. / Xiao, Y.Z. / Li, R. / Liu, Y. / Long, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ah8.cif.gz | 358.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ah8.ent.gz | 292.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ah8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/6ah8 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/6ah8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ah7C 4zwoS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 51639.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas lipolytica (bacteria) Gene: pepQ, SAMN04487854_12236 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I7CHQ2, Xaa-Pro dipeptidase #2: Chemical | ChemComp-MN / #3: Chemical | #4: 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: 2.83 Å3/Da / Density % sol: 56.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M Ammonium sulfate, 5% PEG400, 100 mM MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 70044 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2 / Num. unique obs: 6932 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZWO Resolution: 2.61→44.53 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.959 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.757 / ESU R Free: 0.345 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.136 Å2
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Refinement step | Cycle: 1 / Resolution: 2.61→44.53 Å
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Refine LS restraints |
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