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Open data
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Basic information
Entry | Database: PDB / ID: 1bsk | ||||||
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Title | ZINC DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI | ||||||
![]() | PROTEIN (PEPTIDE DEFORMYLASE) | ||||||
![]() | HYDROLASE / DEFORMYLASE / INHIBITOR / METALLOPROTEINASE | ||||||
Function / homology | ![]() co-translational protein modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Hao, B. / Gong, W. / Rajagopalan, P.T. / Hu, Y. / Pei, D. / Chan, M.K. | ||||||
![]() | ![]() Title: Structural basis for the design of antibiotics targeting peptide deformylase. Authors: Hao, B. / Gong, W. / Rajagopalan, P.T. / Zhou, Y. / Pei, D. / Chan, M.K. #1: ![]() Title: Crystal Structure of the Escherichia Coli Peptide Deformylase Authors: Chan, M.K. / Gong, W. / Rajagopalan, P.T. / Hao, B. / Tsai, C. / Pei, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.3 KB | Display | ![]() |
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PDB format | ![]() | 32.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
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Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bsjC ![]() 1dffS S: Starting model for refinement C: citing same article ( |
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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: 19226.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-MLN / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 6118 / % possible obs: 88.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Rsym value: 10 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.281 / % possible all: 76.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 10960 / % possible obs: 85.2 % / Num. measured all: 58431 / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.48 Å / % possible obs: 86.3 % / Rmerge(I) obs: 0.24 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DFF Resolution: 3→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.14 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. reflection obs: 10960 / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 3 Å / Rfactor Rfree: 0.285 / % reflection Rfree: 6.3 % / Rfactor Rwork: 0.233 |