+Open data
-Basic information
Entry | Database: PDB / ID: 7sfm | ||||||
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Title | Mycobacterium tuberculosis Hip1 crystal structure | ||||||
Components | Hip1 | ||||||
Keywords | HYDROLASE / Mtb / AEBSF / TB / Tuberculosis / serine hydrolase | ||||||
Function / homology | Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / Hydrolases; Acting on peptide bonds (peptidases) / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / peptidase activity / Alpha/Beta hydrolase fold / proteolysis / ACETATE ION / Protease Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å | ||||||
Authors | Ostrov, D.A. / Li, D. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: 2.1 angstrom crystal structure of the Mycobacterium tuberculosis serine hydrolase, Hip1, in its anhydro-form (Anhydrohip1). Authors: Brooks, C.L. / Ostrov, D.A. / Schumann, N.C. / Kakkad, S. / Li, D. / Pena, K. / Williams, B.P. / Goldfarb, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sfm.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sfm.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 7sfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sfm_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7sfm_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7sfm_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 7sfm_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/7sfm ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sfm | HTTPS FTP |
-Related structure data
Related structure data | 8e5wC 5ugqS S: Starting model for refinement C: citing same article (ref.) |
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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: 51656.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tap / Production host: Escherichia coli (E. coli) References: UniProt: A0A654TLU9, Hydrolases; Acting on peptide bonds (peptidases), Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | 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: 3.95 Å3/Da / Density % sol: 68.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 30% PEG 3350, 0.1M sodium acetate pH 5.6, 0.2 M ammonium sulfate and 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9436 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9436 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→29.464 Å / Num. obs: 44555 / % possible obs: 99 % / Redundancy: 1.1 % / Rrim(I) all: 1.72E-17 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.149→2.23 Å / Num. unique obs: 4379 / Rrim(I) all: 1.59E-17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UGQ Resolution: 2.149→29.464 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / 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: 76.23 Å2 / Biso mean: 24.7479 Å2 / Biso min: 10.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.149→29.464 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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