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- PDB-3ta8: Crystal structure HP-NAP from strain YS39 iron loaded (cocrystall... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ta8 | ||||||
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Title | Crystal structure HP-NAP from strain YS39 iron loaded (cocrystallization 5mM) | ||||||
![]() | Neutrophil-activating protein | ||||||
![]() | METAL TRANSPORT / DODECAMER / FOUR-HELIX BUNDLE | ||||||
Function / homology | ![]() oxidoreductase activity, acting on metal ions / ferric iron binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tsuruta, O. / Yokoyama, H. / Fujii, S. | ||||||
![]() | ![]() Title: A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP) Authors: Tsuruta, O. / Yokoyama, H. / Fujii, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.5 KB | Display | ![]() |
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PDB format | ![]() | 33.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.3 KB | Display | ![]() |
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Full document | ![]() | 432.5 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3t9jC ![]() 1ji4S C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19006.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.1M L-arginine, 20% ethylene glycol, 0.01M ferrous sulfate , pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2010 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 10455 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 39.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.92 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JI4 Resolution: 2.5→38.49 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.021 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.625 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→38.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.503→2.568 Å / Total num. of bins used: 20
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