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- PDB-6nb1: Crystal structure of Escherichia coli ClpP protease complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nb1 | |||||||||
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Title | Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06 | |||||||||
![]() | ATP-dependent Clp protease proteolytic subunit![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mabanglo, M.F. / Houry, W.A. / Eger, B.T. / Bryson, S. / Pai, E.F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Authors: Mabanglo, M.F. / Leung, E. / Vahidi, S. / Seraphim, T.V. / Eger, B.T. / Bryson, S. / Bhandari, V. / Zhou, J.L. / Mao, Y.Q. / Rizzolo, K. / Barghash, M.M. / Goodreid, J.D. / Phanse, S. / ...Authors: Mabanglo, M.F. / Leung, E. / Vahidi, S. / Seraphim, T.V. / Eger, B.T. / Bryson, S. / Bhandari, V. / Zhou, J.L. / Mao, Y.Q. / Rizzolo, K. / Barghash, M.M. / Goodreid, J.D. / Phanse, S. / Babu, M. / Barbosa, L.R.S. / Ramos, C.H.I. / Batey, R.A. / Kay, L.E. / Pai, E.F. / Houry, W.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 532.8 KB | Display | ![]() |
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PDB format | ![]() | 443.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6nahC ![]() 6naqC ![]() 6nawC ![]() 6nayC ![]() 1yg6S 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: 23212.650 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: K12 / Gene: clpP, lopP, b0437, JW0427 / Production host: ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-KHS / #3: Chemical | ChemComp-GOL / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 51-63% MPD 0.1 M sodium acetate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→48.002 Å / Num. obs: 225772 / % possible obs: 98.3 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 6914 / CC1/2: 0.702 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1YG6 Resolution: 1.9→48 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48 Å
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Refine LS restraints |
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LS refinement shell |
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