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Yorodumi- PDB-6yug: Crystal structure of C. parvum GNA1 in complex with acetyl-CoA an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yug | ||||||
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Title | Crystal structure of C. parvum GNA1 in complex with acetyl-CoA and glucose 6P. | ||||||
Components | Diamine acetyltransferase | ||||||
Keywords | TRANSFERASE / Acyltransferase / GNA1 / C. parvum | ||||||
Function / homology | Function and homology information spermine acetylation / spermidine acetylation / putrescine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum Iowa II (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.95 Å | ||||||
Authors | Chi, J. / Cova, M. / de las Rivas, M. / Medina, A. / Borges, R. / Leivar, P. / Planas, A. / Uson, I. / Hurtado-Guerrero, R. / Izquierdo, L. | ||||||
Citation | Journal: Mbio / Year: 2020 Title: Plasmodium falciparum Apicomplexan-Specific Glucosamine-6-Phosphate N -Acetyltransferase Is Key for Amino Sugar Metabolism and Asexual Blood Stage Development. Authors: Chi, J. / Cova, M. / de Las Rivas, M. / Medina, A. / Borges, R.J. / Leivar, P. / Planas, A. / Uson, I. / Hurtado-Guerrero, R. / Izquierdo, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yug.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yug.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 6yug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yug ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yug | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17865.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum Iowa II (eukaryote) Gene: SSAT, cgd4_4000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CPU3, diamine N-acetyltransferase #2: Chemical | #3: Sugar | ChemComp-G6P / | #4: Water | ChemComp-HOH / | 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: 1.96 Å3/Da / Density % sol: 37.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: NH4Cl HEPES glycerolethoxilate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.773 Å / Num. obs: 20192 / % possible obs: 95.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.95→2.06 Å / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2638 / CC1/2: 0.852 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.95→19.773 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.773 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.1305 Å / Origin y: -5.8962 Å / Origin z: 17.3111 Å
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Refinement TLS group | Selection details: all |