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Yorodumi- PDB-8fbu: Crystal structure of Cryptosporidium parvum N-myristoyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fbu | |||||||||
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Title | Crystal structure of Cryptosporidium parvum N-myristoyltransferase with bound myristoyl-CoA and Compound-2 | |||||||||
Components | Glycylpeptide N-tetradecanoyltransferase | |||||||||
Keywords | TRANSFERASE/INHIBITOR / NMT / inhibitor / Myristoyl-CoA / MyrCoA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSFERASE / TRANSFERASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Cryptosporidium parvum Iowa II (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Staker, B.L. / Fenwick, M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fbu.cif.gz | 554.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fbu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fbu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8fbu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8fbu_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 8fbu_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/8fbu ftp://data.pdbj.org/pub/pdb/validation_reports/fb/8fbu | HTTPS FTP |
-Related structure data
Related structure data | 8fbmC 8fbtC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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 AB
#1: Protein | Mass: 50717.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote) Gene: cgd3_320 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q5CV46 |
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-Non-polymers , 8 types, 588 molecules
#2: Chemical | #3: Chemical | ChemComp-XOL / ( | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 1.0 mM compound at 4C for 30 min, then mixed with 1:1 with 100 mM BisTris-HCl pH 6. ...Details: CrpaA.18219.a.A10.PS38408 at 17.5 mg/mL was incubated with final concentrations of 0.8 mM Myristoyl-CoA and 1.0 mM compound at 4C for 30 min, then mixed with 1:1 with 100 mM BisTris-HCl pH 6.5 and 27.5% PEG 3350. Protein buffer is 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide. Crystals are harvested using crystallant plus 25% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 59810 / % possible obs: 97.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.23 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 1.44 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2994 / CC1/2: 0.504 / CC star: 0.819 / Rpim(I) all: 0.506 / Rrim(I) all: 0.927 / Χ2: 0.778 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.37 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→35.37 Å
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Refine LS restraints |
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LS refinement shell |
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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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