+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yey | ||||||
---|---|---|---|---|---|---|---|
Title | HUaa-20bp | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / HU-DNA / transcription / pathogenicity / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() 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 / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hammel, M. / Reyes, F.E. / Parpana, R. / Tainer, J.A. / Adhya, S. / Amlanjyoti, D. | ||||||
![]() | ![]() Title: HU multimerization shift controls nucleoid compaction. Authors: Hammel, M. / Amlanjyoti, D. / Reyes, F.E. / Chen, J.H. / Parpana, R. / Tang, H.Y. / Larabell, C.A. / Tainer, J.A. / Adhya, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yewC ![]() 4yexC ![]() 4yf0C ![]() 4yfhC ![]() 4yftC ![]() 1mulS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 9621.058 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 4307.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: DNA chain | | Mass: 4292.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() Sequence details | DNA sample sequence used in experiment is 5'-GTTCAATTGTTGTTAACTTG-3'. But the asymmetric unit ...DNA sample sequence used in experiment is 5'-GTTCAATTGT | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 45% 2-Methyl-2,4-pentadiol, 0.2M NH4F |
-Data collection
Diffraction | Mean temperature: 93.15 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013 / Details: Q315R |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.354→58.08 Å / Num. all: 4566 / Num. obs: 4566 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.03 / Num. measured all: 16115 |
Reflection shell | Resolution: 3.354→3.368 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.701 / % possible all: 98 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1MUL Resolution: 3.354→58.08 Å / Cor.coef. Fo:Fc: 0.9115 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.53 Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all ...Details: The asymmetric unit of the crystal contains multiple, out-of-register duplex positions, such that backbones superimpose, but base identity differs. The density is an average of all nucleotides, and the DNA chain was built accordingly.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 218.82 Å2 / Biso mean: 150.232 Å2 / Biso min: 94.58 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.354→58.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.35→3.75 Å / Total num. of bins used: 5
|