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- PDB-7t3v: Metal dependent activation of Plasmodium falciparum M17 aminopept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t3v | ||||||
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Title | Metal dependent activation of Plasmodium falciparum M17 aminopeptidase, spacegroup P22121 after crystals soaked with Zn2+ | ||||||
![]() | M17 leucyl aminopeptidase | ||||||
![]() | HYDROLASE / Metallo aminopeptidase / malaria / PEPTIDE BINDING PROTEIN | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Webb, C.T. / McGowan, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase. Authors: Webb, C.T. / Yang, W. / Riley, B.T. / Hayes, B.K. / Sivaraman, K.K. / Malcolm, T.R. / Harrop, S. / Atkinson, S.C. / Kass, I. / Buckle, A.M. / Drinkwater, N. / McGowan, 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 | ![]() | 716.4 KB | Display | ![]() |
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PDB format | ![]() | 470.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7srvSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 58577.777 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 301 molecules ![](data/chem/img/CO3.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CO3 / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM HEPES pH 8.0, 150 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.26 Å / Num. obs: 144874 / % possible obs: 95.49 % / Redundancy: 9.7 % / Biso Wilson estimate: 44.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1411 / Net I/σ(I): 11.81 |
Reflection shell | Resolution: 2.3→2.385 Å / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 14859 / CC1/2: 0.743 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7SRV Resolution: 2.3→47.24 Å / SU ML: 0.3574 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.6706 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.24 Å
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Refine LS restraints |
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LS refinement shell |
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