+Open data
-Basic information
Entry | Database: PDB / ID: 8h5z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of RadD/ATP analogue complex | ||||||
Components | Putative DNA repair helicase RadD | ||||||
Keywords | DNA BINDING PROTEIN / helicase superfamily 2 DNA repair ATPase | ||||||
Function / homology | Function and homology information postreplication repair / response to ionizing radiation / helicase activity / double-strand break repair / single-stranded DNA binding / DNA helicase / response to xenobiotic stimulus / translation / cell division / ATP hydrolysis activity ...postreplication repair / response to ionizing radiation / helicase activity / double-strand break repair / single-stranded DNA binding / DNA helicase / response to xenobiotic stimulus / translation / cell division / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00002725136 Å | ||||||
Authors | Yan, X.X. / Tian, L.F. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Int J Mol Sci / Year: 2023 Title: Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli. Authors: Tian, L.F. / Kuang, X. / Ding, K. / Gao, H. / Tang, Q. / Yan, X.X. / Xu, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8h5z.cif.gz | 232.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8h5z.ent.gz | 181.7 KB | Display | PDB format |
PDBx/mmJSON format | 8h5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/8h5z ftp://data.pdbj.org/pub/pdb/validation_reports/h5/8h5z | HTTPS FTP |
---|
-Related structure data
Related structure data | 8h5yC 6jdeS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66509.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: radD, yejH, yejI, yejJ, b2184, JW2172 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P33919, DNA helicase #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
---|---|
Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / Details: 500 mM NaCl, 5 mM MgCl2 and 18% [w/v] PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 38570 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 68.6097829319 Å2 / CC1/2: 0.795 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3→3.12 Å / Num. unique obs: 1910 / CC1/2: 0.795 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JDE Resolution: 3.00002725136→19.9761477285 Å / SU ML: 0.417256574005 / Cross valid method: FREE R-VALUE / σ(F): 1.35546330902 / Phase error: 33.7639508679 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.9507554787 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.00002725136→19.9761477285 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|