+Open data
-Basic information
Entry | Database: PDB / ID: 1jts | ||||||
---|---|---|---|---|---|---|---|
Title | DNA PROTECTION AND BINDING BY E. COLI DPS PROTEIN | ||||||
Components | DNA PROTECTION DURING STARVATION PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / DODECAMER | ||||||
Function / homology | Function and homology information DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Luo, J. / Liu, D. / White, M.A. / Fox, R.O. | ||||||
Citation | Journal: To be Published Title: DNA Protection and Binding by E. Coli Dps Protein Authors: Luo, J. / Liu, D. / White, M.A. / Fox, R.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jts.cif.gz | 709 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jts.ent.gz | 593 KB | Display | PDB format |
PDBx/mmJSON format | 1jts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jts_validation.pdf.gz | 661.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jts_full_validation.pdf.gz | 793.7 KB | Display | |
Data in XML | 1jts_validation.xml.gz | 141.7 KB | Display | |
Data in CIF | 1jts_validation.cif.gz | 186.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jts ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jts | HTTPS FTP |
-Related structure data
Related structure data | 1jreC 1l8hC 1l8iC 1f33S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dodecamer. The unit cell contains two dodecamers: chains A-L and chains M-X. |
-Components
#1: Protein | Mass: 18664.340 Da / Num. of mol.: 24 / Mutation: D75C, D78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Dps / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABT2 #2: Chemical | ChemComp-TRS / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 55 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 10MM MOPS, 100MM KCL, 10% GLYCEROL + 100MM TRISHCL, 100MM KCL, 10% GLYCEROL, 11% PEG 8000, AND 5MM DTT, pH 8.10, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 128142 / Num. obs: 128142 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.81 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.22 / % possible all: 87.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F33 Resolution: 2.6→29.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2534419.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1617 Å2 / ksol: 0.352421 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.64 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|