+Open data
-Basic information
Entry | Database: PDB / ID: 1l8i | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l8i.cif.gz | 365.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l8i.ent.gz | 301.1 KB | Display | PDB format |
PDBx/mmJSON format | 1l8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l8i_validation.pdf.gz | 547.4 KB | Display | wwPDB validaton report |
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Full document | 1l8i_full_validation.pdf.gz | 611.8 KB | Display | |
Data in XML | 1l8i_validation.xml.gz | 71.5 KB | Display | |
Data in CIF | 1l8i_validation.cif.gz | 94 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8i ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8i | HTTPS FTP |
-Related structure data
Related structure data | 1jreC 1jtsC 1l8hC 1f33S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The dodecamer is the biological assembly |
-Components
#1: Protein | Mass: 18664.340 Da / Num. of mol.: 12 / Mutation: D75C, D78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABT2 #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-TRS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.5 % |
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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 |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 6, 1998 / Details: MAXOS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→90 Å / Num. all: 42543 / Num. obs: 41406 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.12 % / Rmerge(I) obs: 0.283 / Num. unique all: 4031 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F33 Resolution: 3→29.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3516946.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.1092 Å2 / ksol: 0.331926 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→29.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.05 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 20
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Xplor file |
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