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Yorodumi- PDB-7zm2: Crystal structure of HsaD from Mycobacterium tuberculosis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zm2 | ||||||
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Title | Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclophostin-like inhibitor CyC8b | ||||||
Components | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | ||||||
Keywords | HYDROLASE / HsaD / M. tuberculosis / cholesterol / inhibitor | ||||||
Function / homology | Function and homology information 4,9-DSHA hydrolase activity / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / biological process involved in interaction with host / steroid biosynthetic process / : / lipid catabolic process / peptidoglycan-based cell wall / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Barelier, S. / Roig-Zamboni, V. / Cavalier, J.F. / Sulzenbacher, G. | ||||||
Funding support | France, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis. Authors: Barelier, S. / Avellan, R. / Gnawali, G.R. / Fourquet, P. / Roig-Zamboni, V. / Poncin, I. / Point, V. / Bourne, Y. / Audebert, S. / Camoin, L. / Spilling, C.D. / Canaan, S. / Cavalier, J.F. / Sulzenbacher, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zm2.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zm2.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 7zm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/7zm2 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zm2 | HTTPS FTP |
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-Related structure data
Related structure data | 7zjtSC 7zm1C 7zm3C 7zm4C 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: 32986.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: hsaD, bphD, Rv3569c Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: P9WNH5, 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES Na 0.1 M NH4SO4 1.656 M PEG400 5.76% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980114 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.980114 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→45.26 Å / Num. obs: 36843 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.436 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.048 / Rrim(I) all: 0.165 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZJT Resolution: 2.2→45.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.451 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.47 Å2 / Biso mean: 36.045 Å2 / Biso min: 10.72 Å2
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Refinement step | Cycle: final / Resolution: 2.2→45.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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