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Yorodumi- PDB-1dps: THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dps | ||||||
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Title | THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA | ||||||
Components | DPS | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING PROTEIN / FERRITIN / IRON SEQUESTRATION / STATIONARY PHASE / OXIDATIVE DAMAGE | ||||||
Function / homology | Function and homology information DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / response to stress / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / response to stress / 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 / MIR, NCS / Resolution: 1.6 Å | ||||||
Authors | Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dps.cif.gz | 383.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dps.ent.gz | 315.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dps_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 1dps_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 1dps_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 1dps_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dps ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dps | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 18736.359 Da / Num. of mol.: 12 / Mutation: S164C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ZK126 DPS\:\:KAN / Gene: DPS / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABT2 #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 53 % / Description: FUJI IMAGE PLATES FOR CHESS DATA |
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Crystal grow | pH: 8 Details: 1.55-1.7 M SODIUM FORMATE 13-16% PEG 8000 100 MM NACL 50 MM TRIS PH 8, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 1792266 / % possible obs: 92 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.052 / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR, NCS / Resolution: 1.6→20 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 18.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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Xplor file |
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