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Yorodumi- PDB-4s01: Crystal structure of metallopeptidase-like dimethylsulphoniopropi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s01 | ||||||
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Title | Crystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP mutant D377N in complex with acrylate | ||||||
Components | Peptidase M24 | ||||||
Keywords | LYASE / metallopeptidase-like DMSP lyase / DMSP lyase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Silicibacter lacuscaerulensis ITI-1157 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zhang, Y. / Wang, P. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2015 Title: Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold. Authors: Wang, P. / Chen, X.L. / Li, C.Y. / Gao, X. / Zhu, D.Y. / Xie, B.B. / Qin, Q.L. / Zhang, X.Y. / Su, H.N. / Zhou, B.C. / Xun, L.Y. / Zhang, Y.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s01.cif.gz | 388.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s01.ent.gz | 315.5 KB | Display | PDB format |
PDBx/mmJSON format | 4s01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/4s01 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/4s01 | 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: 50463.125 Da / Num. of mol.: 4 / Mutation: D377N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter lacuscaerulensis ITI-1157 (bacteria) Gene: SL1157_2466 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CY07 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-AKR / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.86 Å3/Da / Density % sol: 74.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M potassium/sodium phosphate, pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 219859 / Num. obs: 219859 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 99 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.315 Å / SU ML: 0.25 / σ(F): 1.96 / Phase error: 23.03 / 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: 2.1→34.315 Å
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Refine LS restraints |
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LS refinement shell |
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