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Yorodumi- PDB-3ge4: Crystal structure of ferritin:DNA-binding protein DPS from Brucel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ge4 | ||||||
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Title | Crystal structure of ferritin:DNA-binding protein DPS from Brucella Melitensis | ||||||
Components | DNA PROTECTION DURING STARVATION PROTEIN | ||||||
Keywords | DNA BINDING PROTEIN / SSGCID / FERRITIN / DNA-BINDING PROTEIN / DPS / BURKHOLDERIA PSEUDOMALLEI / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ferritin:DNA-binding protein DPS from Brucella Melitensis Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ge4.cif.gz | 426.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ge4.ent.gz | 346.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ge4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/3ge4 ftp://data.pdbj.org/pub/pdb/validation_reports/ge/3ge4 | HTTPS FTP |
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-Related structure data
Related structure data | 1o9rS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19309.736 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 1719B / Gene: BMEI1980 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YE98 #2: Chemical | ChemComp-CA / #3: 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: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: PACT SCREEN, E2: 20% PEG 3350, 200MM NABR, BRABA.00136.A AT 24.4MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 212707 / Num. obs: 212707 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 20.38 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.35 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.1 / Num. unique all: 15695 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1o9r dodecamer, modified with ccp4 program chainsaw Resolution: 1.7→19.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.855 / SU ML: 0.06 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
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