+Open data
-Basic information
Entry | Database: PDB / ID: 6jq1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of DdrO from Deinococcus geothermalis | ||||||
Components | Transcriptional regulator, XRE family | ||||||
Keywords | DNA BINDING PROTEIN / Transcription factor / Xre / HTH / Dimerization | ||||||
Function / homology | Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / : / Transcriptional regulator, XRE family Function and homology information | ||||||
Biological species | Deinococcus geothermalis DSM 11300 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Lu, H. / Hua, Y. / Zhao, Y. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO. Authors: Lu, H. / Wang, L. / Li, S. / Pan, C. / Cheng, K. / Luo, Y. / Xu, H. / Tian, B. / Zhao, Y. / Hua, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6jq1.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6jq1.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jq1_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6jq1_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 6jq1_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 6jq1_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/6jq1 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/6jq1 | HTTPS FTP |
-Related structure data
Related structure data | 4pu7S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14930.978 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus geothermalis DSM 11300 (bacteria) Strain: DSM 11300 / Gene: Dgeo_0336 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q1J1J5 #2: Chemical | ChemComp-LI / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % |
---|---|
Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 / Details: LiCl, HEPES |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 16314 / % possible obs: 98.7 % / Redundancy: 4.67 % / Biso Wilson estimate: 57.15 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.88 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.48 % / Rmerge(I) obs: 0.692 / Num. unique obs: 1177 / % possible all: 96.9 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PU7 Resolution: 2.3→30 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.06
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 12.6293 Å / Origin y: 30.2647 Å / Origin z: 58.6735 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |