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Yorodumi- PDB-2os3: Structures of actinonin bound peptide deformylases from E. faecal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2os3 | ||||||
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Title | Structures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes | ||||||
Components | Peptide deformylase | ||||||
Keywords | HYDROLASE / PDF / peptide deformylase | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes M1 GAS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Kim, E.E. / Kim, K.-H. / Moon, J.H. / Choi, K. / Lee, H.K. / Parh, H.S. | ||||||
Citation | Journal: To be Published Title: Structures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes Authors: Kim, E.E. / Kim, K.-H. / Moon, J.H. / Choi, K. / Lee, H.K. / Park, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2os3.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2os3.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 2os3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/2os3 ftp://data.pdbj.org/pub/pdb/validation_reports/os/2os3 | HTTPS FTP |
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-Related structure data
Related structure data | 2os0C 2os1C 1lqyS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23004.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes M1 GAS (bacteria) Species: Streptococcus pyogenes / Strain: ATCC 700294 / Gene: def / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P68771, peptide deformylase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-BB2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 4000, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å |
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Feb 22, 2005 / Details: mirrors |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 13084 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.1→2.28 Å / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LQY Resolution: 2.26→19.94 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 288722.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.8706 Å2 / ksol: 0.358824 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.26→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.4 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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Xplor file |
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