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Yorodumi- PDB-8f5v: Crystal structure of Mycobacterium tuberculosis Mycothiol S-trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f5v | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Mycothiol S-transferase enzyme in complex with mycothiol and Zn2+ | ||||||
Components | Conserved protein | ||||||
Keywords | TRANSFERASE / DinB superfamily / Mycothiol / ternary complex / metalloenzyme | ||||||
Function / homology | Protein of unknown function DUF664 / Protein of unknown function (DUF664) / DinB/YfiT-like putative metalloenzymes / Mycothiol / Conserved protein Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Jayasinghe, Y.P. / Ronning, D.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Rsc Med Chem / Year: 2023 Title: The Mycobacterium tuberculosis mycothiol S -transferase is divalent metal-dependent for mycothiol binding and transfer. Authors: Jayasinghe, Y.P. / Banco, M.T. / Lindenberger, J.J. / Favrot, L. / Palcekova, Z. / Jackson, M. / Manabe, S. / Ronning, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f5v.cif.gz | 160.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f5v.ent.gz | 124.9 KB | Display | PDB format |
PDBx/mmJSON format | 8f5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f5v_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8f5v_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8f5v_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 8f5v_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f5v ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f5v | HTTPS FTP |
-Related structure data
Related structure data | 8fx9C 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: 18518.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0443 / Production host: Escherichia coli (E. coli) / References: UniProt: O53728 #2: Chemical | #3: Chemical | ChemComp-ZN / #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: 2.07 Å3/Da / Density % sol: 40.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris pH 6.5, 0.2 M Magnesium chloride hexahydrate, 16% Polyethylene glycol 3350, 0.1 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.00799 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00799 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→53.64 Å / Num. obs: 53687 / % possible obs: 97.4 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 0.88 / Net I/σ(I): 16.3 / Num. measured all: 661343 |
Reflection shell | Resolution: 1.45→1.53 Å / % possible obs: 84.4 % / Redundancy: 8 % / Rmerge(I) obs: 0.675 / Num. measured all: 53447 / Num. unique obs: 6675 / CC1/2: 0.878 / Rpim(I) all: 0.249 / Rrim(I) all: 0.722 / Χ2: 0.64 / Net I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Mtb_MST apo structure Resolution: 1.45→33.7 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.97 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→33.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.7582 Å / Origin y: 18.0481 Å / Origin z: -13.2404 Å
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Refinement TLS group | Selection details: all |