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- PDB-4pt4: Crystal structure Analysis of N terminal region containing the di... -
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Basic information
Entry | Database: PDB / ID: 4pt4 | |||||||||
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Title | Crystal structure Analysis of N terminal region containing the dimerization domain and DNA binding domain of HU protein(Histone like protein-DNA binding) from Mycobacterium tuberculosis [H37Ra] | |||||||||
![]() | DNA-binding protein HU homolog | |||||||||
![]() | DNA BINDING PROTEIN / DIMERIZATION BY FOUR HELIX BUNDLE INTERACTION / DNA condensation / DNA-binding | |||||||||
Function / homology | ![]() nucleoid organization / biofilm matrix assembly / cellular response to iron ion starvation / DNA protection / nucleoid / supercoiled DNA binding / chromosome condensation / DNA-binding transcription activator activity / ferroxidase / ferroxidase activity ...nucleoid organization / biofilm matrix assembly / cellular response to iron ion starvation / DNA protection / nucleoid / supercoiled DNA binding / chromosome condensation / DNA-binding transcription activator activity / ferroxidase / ferroxidase activity / peptidoglycan-based cell wall / ferric iron binding / protein-DNA complex / cell wall organization / structural constituent of chromatin / iron ion transport / double-stranded DNA binding / intracellular iron ion homeostasis / damaged DNA binding / oxidoreductase activity / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / DNA binding / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bhowmick, T. / Ramagopal, U.A. / Ghosh, S. / Nagaraja, V. / Ramakumar, S. | |||||||||
![]() | ![]() Title: Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors Authors: Bhowmick, T. / Ghosh, S. / Dixit, K. / Ganesan, V. / Ramagopal, U.A. / Dey, D. / Sarma, S.P. / Ramakumar, S. / Nagaraja, V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 64.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4dkyC ![]() 1p71S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10672.215 Da / Num. of mol.: 2 Fragment: N terminal UNP residues 1-99 (dimerization domain and DNA binding domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hupB, MRA_3015 / Plasmid: pET20b / Production host: ![]() ![]() #2: Chemical | ChemComp-FMT / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.13 % / Mosaicity: 1.172 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 3M Sodium formate, 0.1M Tris-Cl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2007 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator (Cryogenically cooled) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→50 Å / Num. obs: 10304 / % possible obs: 98.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Χ2: 1.078 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P71 Resolution: 2.04→41.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2366 / WRfactor Rwork: 0.1766 / FOM work R set: 0.7719 / SU B: 15.753 / SU ML: 0.183 / SU R Cruickshank DPI: 0.2594 / SU Rfree: 0.2072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 82.19 Å2 / Biso mean: 34.753 Å2 / Biso min: 18.77 Å2
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Refine analyze | Luzzati coordinate error obs: 0.249 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→41.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.037→2.09 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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