+Open data
-Basic information
Entry | Database: PDB / ID: 4nun | ||||||
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Title | Crystal structure of copper-bound Na-ASP-2 | ||||||
Components | Ancylostoma secreted protein 2 | ||||||
Keywords | UNKNOWN FUNCTION / SCP/TAPS / Excretory/secretory product | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Necator americanus (New World hookworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hofmann, A. | ||||||
Citation | Journal: Int.J.Biochem.Cell Biol. / Year: 2014 Title: Probing the equatorial groove of the hookworm protein and vaccine candidate antigen, Na-ASP-2. Authors: Mason, L. / Tribolet, L. / Simon, A. / von Gnielinski, N. / Nienaber, L. / Taylor, P. / Willis, C. / Jones, M.K. / Sternberg, P.W. / Gasser, R.B. / Loukas, A. / Hofmann, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nun.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nun.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/4nun ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nun | HTTPS FTP |
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-Related structure data
Related structure data | 4nuiSC 4nukC 4nuoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22652.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Necator americanus (New World hookworm) Gene: ASP2 / Production host: Pichia pastoris (fungus) / References: UniProt: J9ULM6 |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.89 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 40% PEG4000, 20 mM TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95375 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95375 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29 Å / Num. all: 16083 / Num. obs: 16019 / % possible obs: 99.6 % |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.6 % / Rsym value: 0.219 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4NUI Resolution: 2.2→29 Å / SU ML: 0.26 / σ(F): 1.49 / Phase error: 22.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→29 Å
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Refine LS restraints |
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LS refinement shell |
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