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Open data
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Basic information
Entry | Database: PDB / ID: 2fjc | ||||||
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Title | Crystal structure of antigen TpF1 from Treponema pallidum | ||||||
![]() | Antigen TpF1 | ||||||
![]() | METAL TRANSPORT / Mini ferritin / iron binding protein / antigen | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thumiger, A. / Polenghi, A. / Papinutto, E. / Battistutta, R. / Montecucco, C. / Zanotti, G. | ||||||
![]() | ![]() Title: Crystal structure of antigen TpF1 from Treponema pallidum. Authors: Thumiger, A. / Polenghi, A. / Papinutto, E. / Battistutta, R. / Montecucco, C. / Zanotti, G. #1: ![]() Title: Structure of the neutrophil-activating protein from Helicobacter pylori Authors: Zanotti, G. / Papinutto, E. / Dundon, W. / Battistutta, R. / Seveso, M. / Giudice, G. / Rappuoli, R. / Montecucco, C. #2: ![]() Title: The crystal structure of Dps, a ferritin homologue that binds and protects DNA Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M. #3: ![]() Title: The dodecameric ferritin from listeria innocua contains a novel intersubunit iron-binding site Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D. #4: ![]() Title: Structure of two iron-binding proteins from Bacillus anthracis Authors: Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 466.2 KB | Display | ![]() |
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PDB format | ![]() | 386.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 547.8 KB | Display | ![]() |
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Full document | ![]() | 603.5 KB | Display | |
Data in XML | ![]() | 88.2 KB | Display | |
Data in CIF | ![]() | 118.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ji4S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17252.652 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% PEG 6000, 8% ethylene glycol, 0.1 M Tris buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→185 Å / Num. all: 111030 / Num. obs: 111030 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.5 / Num. unique all: 11886 / % possible all: 70.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1JI4 Resolution: 2.5→59.37 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1010942.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.4013 Å2 / ksol: 0.349013 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→59.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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