+Open data
-Basic information
Entry | Database: PDB / ID: 2o97 | ||||||
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Title | Crystal Structure of E. coli HU heterodimer | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA-binding / heterodimer / DNA structure / DNA supercoiling / E. coli | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Guo, F. / Adhya, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Spiral structure of Escherichia coli HU{alpha}beta provides foundation for DNA supercoiling. Authors: Guo, F. / Adhya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o97.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o97.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 2o97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/2o97 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/2o97 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Four dimers form a tetragonal unit of a spiral filament by symmetry operation. The space group is I41. |
-Components
#1: Protein | Mass: 9549.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupA / Plasmid: pRLM118 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF0 |
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#2: Protein | Mass: 9239.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hupB, hopD / Plasmid: pRLM118 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACF4 |
#3: Chemical | ChemComp-NI / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 0.1M Tris-HCl, 0.01M nickel chloride, 20% PEG-MME2000, 5% glycerol, pH 8.5, EVAPORATION, temperature 298K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 7084 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 6.23 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.362 / % possible all: 64.7 |
-Phasing
Phasing MR | Rfactor: 0.526 / Cor.coef. Fo:Fc: 0.643
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 4583 | ||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 26.752 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.52 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 41.6916 Å / Origin y: 61.3725 Å / Origin z: -1.4093 Å
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Refinement TLS group |
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