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- PDB-4a5a: Crystal structure of the C258S/C268S variant of Toxoplasma gondii... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a5a | ||||||
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Title | Crystal structure of the C258S/C268S variant of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) in complex with magnesium and AMPPNP | ||||||
![]() | NUCLEOSIDE-TRIPHOSPHATASE 1 | ||||||
![]() | HYDROLASE / NTPDASE | ||||||
Function / homology | ![]() symbiont-containing vacuole / protein N-linked glycosylation / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / Golgi apparatus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krug, U. / Zebisch, M. / Straeter, N. | ||||||
![]() | ![]() Title: Structural Insight Into the Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases by Disulfide Reduction. Authors: Krug, U. / Zebisch, M. / Krauss, M. / Straeter, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 899 KB | Display | ![]() |
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PDB format | ![]() | 749.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 82.9 KB | Display | |
Data in CIF | ![]() | 109.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a57SC ![]() 4a59C ![]() 4a5bC 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 67625.789 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ANP / #3: Chemical | ChemComp-MG / Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 258 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 268 TO SER ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.5 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 100 MM KCL, 10 MM MGCL2, 50 MM TRIS PH 8.5, 30% PEG 400, 2 MM AMPPNP AND 10 MM MAGNESIUM ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→39 Å / Num. obs: 61587 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4A57 Resolution: 2.85→40 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.82 / SU B: 42.838 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
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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: 36.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→40 Å
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Refine LS restraints |
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