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- PDB-2os0: Structures of actinonin bound peptide deformylases from E. faecal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2os0 | ||||||
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Title | Structures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes | ||||||
![]() | Peptide deformylase | ||||||
![]() | HYDROLASE / PDF / Peptide deformylase | ||||||
Function / homology | ![]() peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, E.E. / Kim, K.-H. / Moon, J.H. / Choi, K. / Lee, H.K. / Park, H.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.9 KB | Display | ![]() |
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PDB format | ![]() | 38.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 433.9 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2os1C ![]() 2os3C ![]() 1q1yS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21109.068 Da / Num. of mol.: 1 / Mutation: G58D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 15% PEG8000, 0.2M Ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: BRUKER PROTEUM 300 / Detector: CCD / Date: Nov 26, 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: 1.2→50 Å / Num. obs: 58707 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.0915 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / % possible all: 57.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Q1Y Resolution: 1.3→19.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 398911.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.0657 Å2 / ksol: 0.45616 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.3→19.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.38 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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