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Yorodumi- PDB-4ztt: Crystal structures of ferritin mutants reveal diferric-peroxo int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ztt | ||||||
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Title | Crystal structures of ferritin mutants reveal diferric-peroxo intermediates | ||||||
Components | Bacterial non-heme ferritin | ||||||
Keywords | OXIDOREDUCTASE / Helicobactor pylori / Escherichia coli / Gram-negative bacteria / ferritin / iron uptake / ferroxidase center / reaction intermediate | ||||||
Function / homology | Function and homology information bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / cellular response to iron ion / iron ion transport / response to oxidative stress / DNA damage response / identical protein binding ...bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / cellular response to iron ion / iron ion transport / response to oxidative stress / DNA damage response / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli DH1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å | ||||||
Authors | Kim, S. / Park, Y.H. / Jung, S.W. / Seok, J.H. / Chung, Y.B. / Lee, D.B. / Gowda, G. / Lee, J.H. / Han, H.R. / Cho, A.E. ...Kim, S. / Park, Y.H. / Jung, S.W. / Seok, J.H. / Chung, Y.B. / Lee, D.B. / Gowda, G. / Lee, J.H. / Han, H.R. / Cho, A.E. / Lee, C. / Chung, M.S. / Kim, K.H. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2016 Title: Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins from Gram-Negative Bacteria. Authors: Kim, S. / Lee, J.H. / Seok, J.H. / Park, Y.H. / Jung, S.W. / Cho, A.E. / Lee, C. / Chung, M.S. / Kim, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ztt.cif.gz | 244.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ztt.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ztt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/4ztt ftp://data.pdbj.org/pub/pdb/validation_reports/zt/4ztt | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 19571.859 Da / Num. of mol.: 6 / Mutation: S20A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Gene: ftnA, Z2960, ECs2613 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C9QT34, UniProt: P0A998*PLUS, bacterial non-heme ferritin |
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-Non-polymers , 9 types, 920 molecules
#2: Chemical | #3: Chemical | ChemComp-OH / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-FE / #6: Chemical | #7: Chemical | ChemComp-OXY / | #8: Chemical | ChemComp-PER / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.29 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: Lithium sulfate monohydrate, sodium citrate, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 298.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 154787 / % possible obs: 91.6 % / Redundancy: 7.7 % / Net I/σ(I): 17 |
-Processing
Software |
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Refinement | Resolution: 1.83→19.66 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.557 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→19.66 Å
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Refine LS restraints |
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