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Open data
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Basic information
Entry | Database: PDB / ID: 4ly5 | ||||||
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Title | Crystal structure of NaASP2 with Zn2+ | ||||||
![]() | Ancylostoma secreted protein 2 | ||||||
![]() | ANTIBIOTIC / PR1 protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Asojo, O.A. | ||||||
![]() | ![]() Title: Crystal structure of NaASP2 with Zn2+ Authors: Asojo, O.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.1 KB | Display | ![]() |
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PDB format | ![]() | 36.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.7 KB | Display | ![]() |
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Full document | ![]() | 421.2 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u53S 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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Unit cell |
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Components
#1: Protein | Mass: 21214.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ASP2 / References: UniProt: J9ULM6 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.72 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100mM imidazole, 40% PEG 400, 10mM ZnCl2 , pH 8.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→31.6 Å / Num. all: 18323 / Num. obs: 18302 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.832 / Mean I/σ(I) obs: 0.8 / Num. unique all: 874 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1U53 Resolution: 1.664→31.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.52 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.664→31.6 Å
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Refine LS restraints |
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