+Open data
-Basic information
Entry | Database: PDB / ID: 5itj | ||||||
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Title | The structure of histone-like protein | ||||||
Components | AbrB family transcriptional regulator | ||||||
Keywords | DNA BINDING PROTEIN / Histone-like protein / Complex / DNA-binding fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.63 Å | ||||||
Authors | Lin, B.L. / Chen, C.Y. / Huang, C.H. / Ko, T.P. / Chiang, C.H. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Tsai, H.H.G. / Wang, A.H.J. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA. Authors: Lin, B.L. / Chen, C.Y. / Huang, C.H. / Ko, T.P. / Chiang, C.H. / Lin, K.F. / Chang, Y.C. / Lin, P.Y. / Tsai, H.H.G. / Wang, A.H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5itj.cif.gz | 38.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5itj.ent.gz | 25.3 KB | Display | PDB format |
PDBx/mmJSON format | 5itj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5itj_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 5itj_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 5itj_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 5itj_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/5itj ftp://data.pdbj.org/pub/pdb/validation_reports/it/5itj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6283.376 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SULA_1064, SULB_1065, SULC_1064 / Plasmid: pET-29a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3K9N8 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 0.1 M Tris-Cl, 40% PEG 400, 0.2 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→30 Å / Num. obs: 14365 / % possible obs: 97.7 % / Redundancy: 8 % / Net I/σ(I): 44.7 |
Reflection shell | Resolution: 1.63→1.69 Å |
-Processing
Software |
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Refinement | Resolution: 1.63→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.54 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.541 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→30 Å
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Refine LS restraints |
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