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Open data
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Basic information
Entry | Database: PDB / ID: 8rhr | ||||||
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Title | E.coli Peptide Deformylase with bound inhibitor BB4 | ||||||
![]() | Peptide deformylase | ||||||
![]() | HYDROLASE / Peptide Deformylase (EC 3.5.1.88) / Inhibitor | ||||||
Function / homology | peptide deformylase / peptide deformylase activity / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / translation / metal ion binding / 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide / Peptide deformylase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kirschner, H. / Stoll, R. / Hofmann, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase. Authors: Kirschner, H. / Heister, N. / Zouatom, M. / Zhou, T. / Hofmann, E. / Scherkenbeck, J. / Stoll, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19552.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): pET19 with additional TEV protease cutting site Production host: ![]() ![]() |
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-Non-polymers , 5 types, 136 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/BB4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BB4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-BB4 / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, sitting drop Details: 1 ul of protein solution (10 ug/ul) was mixed with 1 ul reservoir solution (0.17 M ammonium sulfate, 25.5% (w/v) PEG4000, 15% (v/v) glycerol); soaking was performed for appr. 22 hours at 291. ...Details: 1 ul of protein solution (10 ug/ul) was mixed with 1 ul reservoir solution (0.17 M ammonium sulfate, 25.5% (w/v) PEG4000, 15% (v/v) glycerol); soaking was performed for appr. 22 hours at 291.2K with 1 ul of stock solution (30 mM) added to the sitting drop well |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 29, 1022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91977 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→46.51 Å / Num. obs: 72634 / % possible obs: 100 % / Redundancy: 36.9 % / Biso Wilson estimate: 23.89 Å2 / CC1/2: 1 / Rrim(I) all: 0.066 / Rsym value: 0.065 / Net I/σ(I): 27.84 |
Reflection shell | Resolution: 1.42→1.46 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5371 / CC1/2: 0.452 / Rrim(I) all: 3.26 / Rsym value: 3.19 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→46.51 Å
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Refine LS restraints |
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LS refinement shell |
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