+Open data
-Basic information
Entry | Database: PDB / ID: 1ji4 | ||||||
---|---|---|---|---|---|---|---|
Title | NAP protein from helicobacter pylori | ||||||
Components | NEUTROPHIL-ACTIVATING PROTEIN A | ||||||
Keywords | METAL TRANSPORT / dodecamer / four-helix bundle | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / : / ferric iron binding / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Zanotti, G. / Papinutto, E. / Dundon, W.G. / Battistutta, R. / Seveso, M. / Del Giudice, G. / Rappuoli, R. / Montecucco, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 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: 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. #2: Journal: Nat.Struct.Biol. / Year: 2000 Title: The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron Binding Site Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ji4.cif.gz | 365.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ji4.ent.gz | 300.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ji4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1ji4 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1ji4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1qghS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16960.396 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: NAPA / Production host: Bacillus subtilis (bacteria) / References: UniProt: P43313 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-UNX / #4: Chemical | ChemComp-MPD / ( #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.44 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.3 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.12 Å2 / ksol: 0.41 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→20.81 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.286 / Rfactor Rwork: 0.278 |