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- PDB-7m7c: Crystal Structure of Hip1 (Rv2224c) mutant - T466A/S228DHA (dehyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m7c | ||||||
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Title | Crystal Structure of Hip1 (Rv2224c) mutant - T466A/S228DHA (dehydroalanine) | ||||||
![]() | Carboxylesterase A | ||||||
![]() | HYDROLASE / serine protease | ||||||
Function / homology | ![]() : / carboxylesterase activity / response to host immune response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / post-translational protein modification / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Naffin-Olivos, J.L. / Daab, A. / Goldfarb, N.E. / Doran, M.H. / Baikovitz, J. / Liu, D. / Sun, S. / White, A. / Dunn, B.M. / Rengarajan, J. ...Naffin-Olivos, J.L. / Daab, A. / Goldfarb, N.E. / Doran, M.H. / Baikovitz, J. / Liu, D. / Sun, S. / White, A. / Dunn, B.M. / Rengarajan, J. / Petsko, G.A. / Ringe, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibitors and Inactivators of Mycobacterium tuberculosis serine protease Hip1 (Rv2224c) Authors: Naffin-Olivos, J.L. / Daab, A. / Goldfarb, N. / Doran, M.H. / Baikovitz, J. / Liu, D. / Sun, S. / White, A. / Dunn, B.M. / Rengarajan, J. / Petsko, G.A. / Ringe, 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 | ![]() | 102.8 KB | Display | ![]() |
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PDB format | ![]() | 75.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5unoS S: Starting model for refinement |
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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
#1: Protein | Mass: 52936.152 Da / Num. of mol.: 1 Mutation: N-terminal truncation of first 49 amino acids, T466A, S228DHA Source method: isolated from a genetically manipulated source Details: N-terminal 6xHis Tag with linker and thrombin recognition cleavage site. Threonine 466 is mutated to alanine. Also residue serine 228 has been modified to dehydroalanine (DHA) Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WHR3, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% (W/V) PEG3350, 0.1 M Sodium Acetate pH 5.6, 0.2 M (NH4)2SO4, 10% (V/V) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.291→50 Å / Num. obs: 37080 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 44.44 Å2 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.095 / Rrim(I) all: 0.26 / Χ2: 0.821 / Net I/σ(I): 2.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UNO Resolution: 2.3→45.358 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.76 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.51 Å2 / Biso mean: 46.7521 Å2 / Biso min: 22.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→45.358 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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