+Open data
-Basic information
Entry | Database: PDB / ID: 4nuo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of zinc-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: 1.75 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4nuo.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4nuo.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 4nuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/4nuo ftp://data.pdbj.org/pub/pdb/validation_reports/nu/4nuo | HTTPS FTP |
---|
-Related structure data
Related structure data | 4nuiSC 4nukC 4nunC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.16 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 34% PEG 4000, 20mM MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.75→28.9 Å / Num. all: 32046 / Num. obs: 31306 / % possible obs: 97.7 % |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 5.6 % / Rsym value: 0.201 / % possible all: 90 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4NUI Resolution: 1.75→28.9 Å / SU ML: 0.13 / σ(F): 1.51 / Phase error: 18.36 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→28.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|