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Yorodumi- PDB-8ioi: Crystal Structure of PadR- family transcriptional regulator Rv117... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ioi | ||||||
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Title | Crystal Structure of PadR- family transcriptional regulator Rv1176c from Mycobacterium tuberculosis H37Rv. | ||||||
Components | PadR family transcriptional regulator | ||||||
Keywords | DNA BINDING PROTEIN / Transcriptional regulator | ||||||
Function / homology | Transcription regulator PadR, C-terminal / Virulence activator alpha C-term / Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / peptidoglycan-based cell wall / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / PadR family transcriptional regulator Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | ||||||
Authors | Yadav, V. / Zohib, M. / Pal, R.K. / Biswal, B.K. / Arora, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Structural and biophysical characterization of PadR family protein Rv1176c of Mycobacterium tuberculosis H37Rv. Authors: Yadav, V. / Zohib, M. / Singh, S. / Pal, R.K. / Tripathi, S. / Jain, A. / Biswal, B.K. / Dasgupta, A. / Arora, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ioi.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ioi.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ioi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ioi_validation.pdf.gz | 641.6 KB | Display | wwPDB validaton report |
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Full document | 8ioi_full_validation.pdf.gz | 650.4 KB | Display | |
Data in XML | 8ioi_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 8ioi_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/8ioi ftp://data.pdbj.org/pub/pdb/validation_reports/io/8ioi | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21464.168 Da / Num. of mol.: 2 / Mutation: C12S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: Rv1176c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O50432 #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-P6G / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.27 Å3/Da / Density % sol: 45.92 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG 400, 0.1M Tris-HCl pH 8.5, 0.1M Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→35 Å / Num. obs: 8284 / % possible obs: 98.5 % / Redundancy: 8.2 % / CC1/2: 0.959 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 2.94→3.05 Å / Num. unique obs: 808 / CC1/2: 0.765 / CC star: 0.931 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→30.16 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.847 / SU B: 21.933 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 40.982 Å2
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Refinement step | Cycle: 1 / Resolution: 2.94→30.16 Å
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