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- PDB-4evc: Crystal Structure HP-NAP from strain YS39 cadmium loaded (Cocryst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4evc | ||||||
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Title | Crystal Structure HP-NAP from strain YS39 cadmium loaded (Cocrystallization 50mM) | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Yokoyama, H. / Tsuruta, O. / Akao, N. / Fujii, S. | ||||||
![]() | ![]() Title: Crystal structure of Helicobacter pylori neutrophil-activating protein with a di-nuclear ferroxidase center in a zinc or cadmium-bound form Authors: Yokoyama, H. / Tsuruta, O. / Akao, N. / Fujii, S. #1: ![]() 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 | ![]() | 47.5 KB | Display | ![]() |
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PDB format | ![]() | 33.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 430.8 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4evbC ![]() 4evdC ![]() 4eveC ![]() 3ta8S S: Starting model for refinement C: citing same article ( |
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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
#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 | ChemComp-CD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50mM cadmium sulfate, 1.0M sodium acetate, 0.1M HEPES-NaOH, 0.1M L-Arginine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→56.3 Å / Num. obs: 11426 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3TA8 Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.857 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 55.65 Å2 / Biso mean: 26.492 Å2 / Biso min: 13.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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