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Yorodumi- PDB-5bkm: Crystal Structure of Hip1 (Rv2224c) mutant - S228DHA (dehydroalanine) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bkm | ||||||
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Title | Crystal Structure of Hip1 (Rv2224c) mutant - S228DHA (dehydroalanine) | ||||||
Components | Carboxylesterase A | ||||||
Keywords | HYDROLASE / serine protease | ||||||
Function / homology | Function and homology information : / 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å | ||||||
Authors | 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 | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of Hip1 (Rv2224c) mutant - S228DHA (dehydroalanine) 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bkm.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bkm.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 5bkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/5bkm ftp://data.pdbj.org/pub/pdb/validation_reports/bk/5bkm | HTTPS FTP |
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-Related structure data
Related structure data | 5unoS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52966.176 Da / Num. of mol.: 1 Mutation: N-terminal truncation of first 49 residues and Serine228 modification to dehydroalanine Source method: isolated from a genetically manipulated source Details: N-terminal 6xHis Tag with linker and thrombin recognition cleavage site. Also residue serine 228 has been modified to dehydroalanine (DHA) Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: caeA, Rv2224c, MTCY427.05c / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.54 % |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.9794 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 22515 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 60.71 Å2 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.1 / Rrim(I) all: 0.314 / Χ2: 0.812 / Net I/σ(I): 2.6 / Num. measured all: 296617 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UNO Resolution: 2.703→45.226 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.3 / 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: 104.12 Å2 / Biso mean: 60.6597 Å2 / Biso min: 41.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.703→45.226 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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