+Open data
-Basic information
Entry | Database: PDB / ID: 6oaj | ||||||
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Title | HUaE34K 19bp SYM DNA | ||||||
Components |
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Keywords | dna binding protein/dna / Nucleoid Associated Protein / DNA supercoiling / Histone like proteins / DNA BINDING PROTEIN / dna binding protein-dna complex | ||||||
Function / homology | Function and homology information HU-DNA complex / DnaA-HU complex / bacterial nucleoid packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding ...HU-DNA complex / DnaA-HU complex / bacterial nucleoid packaging / chromosome condensation / DNA replication initiation / structural constituent of chromatin / DNA repair / DNA-templated transcription / DNA damage response / DNA binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.092 Å | ||||||
Authors | Remesh, S.G. / Hammel, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling. Authors: Remesh, S.G. / Verma, S.C. / Chen, J.H. / Ekman, A.A. / Larabell, C.A. / Adhya, S. / Hammel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oaj.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oaj.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 6oaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/6oaj ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oaj | HTTPS FTP |
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-Related structure data
Related structure data | 6o6kC 6o8qC 4yexS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 9550.046 Da / Num. of mol.: 4 / Mutation: E34K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: hupA, b4000, JW3964 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P0ACF0 #2: DNA chain | | Mass: 5821.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: DNA chain | | Mass: 6119.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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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: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Na-malonate, pH 5.0, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11582 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11582 Å / Relative weight: 1 |
Reflection | Resolution: 4.092→40.492 Å / Num. obs: 4331 / % possible obs: 99.29 % / Redundancy: 6.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.05499 / Rrim(I) all: 0.1316 / Net I/σ(I): 7.28 |
Reflection shell | Resolution: 4.092→4.238 Å / Redundancy: 6 % / Rmerge(I) obs: 1.942 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 406 / CC1/2: 0.479 / Rrim(I) all: 2.129 / % possible all: 98.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YEX Resolution: 4.092→40.492 Å / SU ML: 1.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 48.42 / 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: 4.092→40.492 Å
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Refine LS restraints |
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LS refinement shell |
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