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Yorodumi- PDB-7zhc: Moss spermine/spermidine acetyl transferase (PpSSAT) in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zhc | ||||||
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Title | Moss spermine/spermidine acetyl transferase (PpSSAT) in complex with AcetylCoA and polyethylen glycol | ||||||
Components | N-acetyltransferase domain-containing protein | ||||||
Keywords | TRANSFERASE / SSAT / COENZYME A / ACYLTRANSFERASE | ||||||
Function / homology | N-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / N-acetyltransferase domain-containing protein Function and homology information | ||||||
Biological species | Physcomitrium patens (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.819 Å | ||||||
Authors | Morera, S. / Kopecny, D. / Vigouroux, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Plant J. / Year: 2023 Title: Biochemical and structural basis of polyamine, lysine and ornithine acetylation catalyzed by spermine/spermidine N-acetyl transferase in moss and maize. Authors: Belicek, J. / Luptakova, E. / Kopecny, D. / Frommel, J. / Vigouroux, A. / Cavar Zeljkovic, S. / Jagic, F. / Briozzo, P. / Kopecny, D.J. / Tarkowski, P. / Nisler, J. / De Diego, N. / Morera, S. / Kopecna, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zhc.cif.gz | 178.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zhc.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 7zhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/7zhc ftp://data.pdbj.org/pub/pdb/validation_reports/zh/7zhc | HTTPS FTP |
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-Related structure data
Related structure data | 7zktC 2beiS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 26103.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_008003 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2K1KKM6 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-1PE / | #5: 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: 1.94 Å3/Da / Density % sol: 36.53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000, 10% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.99187 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 1.819→48.89 Å / Num. obs: 23866 / % possible obs: 92.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.819→2.05 Å / Rmerge(I) obs: 1.138 / Num. unique obs: 1194 / CC1/2: 0.497 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BEI Resolution: 1.819→48.89 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.183
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Displacement parameters | Biso max: 81.17 Å2 / Biso mean: 42.44 Å2 / Biso min: 19.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.819→48.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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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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