+Open data
-Basic information
Entry | Database: PDB / ID: 4qjn | ||||||
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Title | Crystal structure of apo nucleoid associated protein, SAV1473 | ||||||
Components | DNA-binding protein HU | ||||||
Keywords | DNA BINDING PROTEIN / DNA condensation / DNA binding | ||||||
Function / homology | Function and homology information chromosome condensation / structural constituent of chromatin / DNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å | ||||||
Authors | Lee, B.-J. / Kim, D.-H. / Im, H. / Yoon, H.-J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: beta-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism Authors: Kim, D.-H. / Im, H. / Jee, J.-G. / Jang, S.-B. / Yoon, H.-J. / Kwon, A.-R. / Kang, S.-M. / Lee, B.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qjn.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qjn.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 4qjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/4qjn ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qjn | HTTPS FTP |
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-Related structure data
Related structure data | 4qjuC 1huuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10713.167 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: hup / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99U17 #2: 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: 2.14 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG2000 monomethyl ether, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 18, 2011 |
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→50 Å / Num. obs: 10877 / Redundancy: 6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 7.2 / Num. unique all: 474 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HUU Resolution: 2.613→30.248 Å / FOM work R set: 0.7466 / SU ML: 0.31 / σ(F): 0 / Phase error: 31.24 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.91 Å2 / Biso mean: 41.78 Å2 / Biso min: 14.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.613→30.248 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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