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- PDB-8fbt: Crystal structure of Cryptosporidium parvum N-myristoyltransferas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fbt | |||||||||
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Title | Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA | |||||||||
![]() | Glycylpeptide N-tetradecanoyltransferase | |||||||||
![]() | TRANSFERASE / NMT / inhibitor / Myristoyl-CoA / MyrCoA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | |||||||||
Function / homology | ![]() glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Staker, B.L. / Fenwick, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA Authors: Staker, B.L. / Fenwick, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 514.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 924.8 KB | Display | ![]() |
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Full document | ![]() | 967.1 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fbmC ![]() 8fbuC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 50714.125 Da / Num. of mol.: 2 / Mutation: K310A, E311A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q5CV46, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 5 types, 342 molecules ![](data/chem/img/MYA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-GOL / | #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: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: CrpaA.18219.a.A42.PS38366 32 mg/mL was incubated with final concentrations of 0.7 mM Myristoyl-CoA at 4C for 30 min, then 0.6 microliter was mixed with 1:1 BisTris-HCl, pH 5.5, 25% PEG 3350. ...Details: CrpaA.18219.a.A42.PS38366 32 mg/mL was incubated with final concentrations of 0.7 mM Myristoyl-CoA at 4C for 30 min, then 0.6 microliter was mixed with 1:1 BisTris-HCl, pH 5.5, 25% PEG 3350. Cryo solution contained crystallant plus 27% PEG-400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999989 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 45534 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Χ2: 0.995 / Net I/σ(I): 19.11 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 2260 / CC1/2: 0.772 / CC star: 0.934 / Rpim(I) all: 0.359 / Rrim(I) all: 0.703 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 41.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→49.83 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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