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Open data
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Basic information
Entry | Database: PDB / ID: 1ji4 | ||||||
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Title | NAP protein from helicobacter pylori | ||||||
![]() | NEUTROPHIL-ACTIVATING PROTEIN A | ||||||
![]() | METAL TRANSPORT / dodecamer / four-helix bundle | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / : / ferric iron binding / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C. | ||||||
![]() | ![]() Title: Structure of the Neutrophil-activating Protein from Helicobacter pylori Authors: Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C. #1: ![]() 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. #2: ![]() Title: The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron Binding Site Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365.7 KB | Display | ![]() |
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PDB format | ![]() | 300.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 553.9 KB | Display | ![]() |
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Full document | ![]() | 627.8 KB | Display | |
Data in XML | ![]() | 77.8 KB | Display | |
Data in CIF | ![]() | 86.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qghS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16960.396 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-UNX / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium acetate, citrate buffer, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 2000 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 71729 / Num. obs: 71729 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 5.9 / Num. unique all: 9698 / % possible all: 90.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Highest resolution: 2.52 Å / % possible obs: 90.9 % / Num. unique obs: 9698 / Rmerge(I) obs: 0.087 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QGH Resolution: 2.52→20.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1727967.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber Details: Only one monomer was treated independently and all the others were generated from the transformation matrices according to the Strict-ncs of CNS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.52→20.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.286 / Rfactor Rwork: 0.278 |