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Yorodumi- PDB-8ypj: Cyrstal structure of the MazE-mt10 Antitoxin from Mycobacterium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ypj | ||||||
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Title | Cyrstal structure of the MazE-mt10 Antitoxin from Mycobacterium tuberculosis | ||||||
Components | Antitoxin | ||||||
Keywords | SIGNALING PROTEIN / Antitoxin / MazE / Mycobacterium tuberculosis / DNA binding | ||||||
Function / homology | Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / regulation of DNA-templated transcription / DNA binding / PHOSPHATE ION / Antitoxin Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Lee, K.Y. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: DNA binding reveals hidden interdomain allostery of a MazE antitoxin from Mycobacterium tuberculosis. Authors: Eun, H.J. / Lee, S.Y. / Lee, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ypj.cif.gz | 33.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ypj.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 8ypj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ypj_validation.pdf.gz | 735.1 KB | Display | wwPDB validaton report |
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Full document | 8ypj_full_validation.pdf.gz | 735.1 KB | Display | |
Data in XML | 8ypj_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 8ypj_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/8ypj ftp://data.pdbj.org/pub/pdb/validation_reports/yp/8ypj | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8141.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A045H4M5 #2: Chemical | ChemComp-PO4 / | #3: 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: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6), 20% (w/v) PEG 6000, 0.2 M NH4Cl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97959 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97959 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→30 Å / Num. obs: 12759 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 0.097 / Num. unique obs: 648 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→30 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.51 / 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: 1.91→30 Å
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Refine LS restraints |
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LS refinement shell |
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