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Yorodumi- PDB-5jz9: Crystal structure of HsaD bound to 3,5-dichloro-4-hydroxybenzenes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jz9 | ||||||
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Title | Crystal structure of HsaD bound to 3,5-dichloro-4-hydroxybenzenesulphonic acid | ||||||
Components | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | ||||||
Keywords | HYDROLASE / HsaD / M. tuberculosis / Cholesterol / Inhibitor / MCP-hydrolase | ||||||
Function / homology | Function and homology information 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 / steroid biosynthetic process / : / lipid catabolic process Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å | ||||||
Authors | Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Sinclair, A. / Eleftheriadou, O. / McHugh, T.D. ...Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Sinclair, A. / Eleftheriadou, O. / McHugh, T.D. / Keany, S. / Lowe, E. / Ballet, R. / Abihammad, A. / Ciulli, A. / Sim, E. | ||||||
Citation | Journal: Br. J. Pharmacol. / Year: 2017 Title: Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach. Authors: Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Eleftheriadou, O. / McHugh, T.D. / Keany, S. / Lowe, E.D. / Ballet, R. / Abuhammad, A. / ...Authors: Ryan, A. / Polycarpou, E. / Lack, N.A. / Evangelopoulos, D. / Sieg, C. / Halman, A. / Bhakta, S. / Eleftheriadou, O. / McHugh, T.D. / Keany, S. / Lowe, E.D. / Ballet, R. / Abuhammad, A. / Jacobs, W.R. / Ciulli, A. / Sim, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jz9.cif.gz | 210.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jz9.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jz9_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 5jz9_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 5jz9_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5jz9_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/5jz9 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/5jz9 | HTTPS FTP |
-Related structure data
Related structure data | 5jzbC 5jzsC 2vf2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 31095.492 Da / Num. of mol.: 2 / Fragment: HsaD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria) Strain: CDC 1551 / Oshkosh / Gene: hsaD, bphD, MT3674 / Plasmid: pVLT31 / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442 References: UniProt: P9WNH4, 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: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 9.5 / Details: 26% (w/v) PEG-3000, 0.1M CHES pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→75.75 Å / Num. obs: 18699 / % possible obs: 99.6 % / Redundancy: 4.4 % / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.68→2.81 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 1.5 / % possible all: 99 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VF2 Resolution: 2.68→75.294 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.5 Å2 / Biso mean: 37.17 Å2 / Biso min: 17.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.68→75.294 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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