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Yorodumi- PDB-3sw8: Strep Peptide Deformylase with a time dependent dichlorobenzamide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sw8 | ||||||
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Title | Strep Peptide Deformylase with a time dependent dichlorobenzamide-reverse hydroxamic acid | ||||||
Components | Peptide deformylase 3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / alpha-beta / peptide deformylase / metal binding protein / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information peptide deformylase / peptide deformylase activity / translation / metal ion binding Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å | ||||||
Authors | Campobasso, N. / Smith, K.J. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors. Authors: Totoritis, R. / Duraiswami, C. / Taylor, A.N. / Kerrigan, J.J. / Campobasso, N. / Smith, K.J. / Ward, P. / King, B.W. / Murrayz-Thompson, M. / Jones, A.D. / Van Aller, G.S. / Aubart, K.M. / ...Authors: Totoritis, R. / Duraiswami, C. / Taylor, A.N. / Kerrigan, J.J. / Campobasso, N. / Smith, K.J. / Ward, P. / King, B.W. / Murrayz-Thompson, M. / Jones, A.D. / Van Aller, G.S. / Aubart, K.M. / Zalacain, M. / Thrall, S.H. / Meek, T.D. / Schwartz, B. #1: Journal: Protein Sci. / Year: 2003 Title: Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species. Authors: Smith, K.J. / Petit, C.M. / Aubart, K. / Smyth, M. / McManus, E. / Jones, J. / Fosberry, A. / Lewis, C. / Lonetto, M. / Christensen, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sw8.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sw8.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 3sw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sw8_validation.pdf.gz | 807.2 KB | Display | wwPDB validaton report |
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Full document | 3sw8_full_validation.pdf.gz | 808.4 KB | Display | |
Data in XML | 3sw8_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 3sw8_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/3sw8 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/3sw8 | HTTPS FTP |
-Related 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: 22721.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: defB, def3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q939R9, peptide deformylase | ||||
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#2: Chemical | ChemComp-NI / | ||||
#3: Chemical | #4: Chemical | ChemComp-5LI / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 1.8 - 2.8 M ammonium sulfate, 1 % - 3 % PEG400, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 |
Detector | Detector: CCD / Date: Jan 26, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. obs: 24582 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→24.125 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 22.46 / 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 / Bsol: 60.761 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.702→24.125 Å
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Refine LS restraints |
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LS refinement shell |
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