[English] 日本語
Yorodumi- PDB-5yx6: Crystal structure of Rv3272 from M. tuberculosis orthorhombic form -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yx6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Rv3272 from M. tuberculosis orthorhombic form | |||||||||
Components | Uncharacterized protein Rv3272 | |||||||||
Keywords | TRANSFERASE / Rv3272 / CoA transferase / fatty acid metabolism / tuberculosis | |||||||||
Function / homology | Transferases; Transferring sulfur-containing groups; CoA-transferases / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / transferase activity / BENZAMIDINE / Probable fatty acyl-CoA transferase Rv3272 Function and homology information | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Ansari, A. / Shrimant, K.S. / Venkatesh Pratap, J. | |||||||||
Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2019 Title: Rv3272 encodes a novel Family III CoA transferase that alters the cell wall lipid profile and protects mycobacteria from acidic and oxidative stress. Authors: Karade, S.S. / Pandey, S. / Ansari, A. / Das, S. / Tripathi, S. / Arora, A. / Chopra, S. / Pratap, J.V. / Dasgupta, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yx6.cif.gz | 280.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yx6.ent.gz | 225.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/5yx6 ftp://data.pdbj.org/pub/pdb/validation_reports/yx/5yx6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5yitSC 5yiyC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42505.445 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv3272 / Production host: Escherichia coli Bl21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P96877 #2: Chemical | ChemComp-BEN / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % / Description: elongated plate-like |
---|---|
Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200mM Disodium hydrogen phosphate, 22% PEG 3350, 2% Benzamidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→46.95 Å / Num. obs: 114403 / % possible obs: 79.8 % / Redundancy: 5.16 % / Biso Wilson estimate: 36.29 Å2 / CC1/2: 0.672 / Rsym value: 0.174 / Net I/σ(I): 7.28 |
Reflection shell | Resolution: 1.87→1.99 Å / CC1/2: 0.25 / Rsym value: 3.5 / % possible all: 21.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YIT Resolution: 2.2→46.95 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.68
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|