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Yorodumi- PDB-8a9n: Structure of DpA polyamine acetyltransferase in complex with 1,3-DAP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a9n | ||||||
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Title | Structure of DpA polyamine acetyltransferase in complex with 1,3-DAP | ||||||
Components | Acetyltransferase | ||||||
Keywords | TRANSFERASE / polyamine acetyltransferase / GNAT / bacterial biofilm formation / Acinetorbacter baumannii | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / membrane Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å | ||||||
Authors | Garcia-Pino, A. / Jurenas, D. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: A polyamine acetyltransferase regulates the motility and biofilm formation of Acinetobacter baumannii. Authors: Armalyte, J. / Cepauskas, A. / Sakalyte, G. / Martinkus, J. / Skerniskyte, J. / Martens, C. / Suziedeliene, E. / Garcia-Pino, A. / Jurenas, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a9n.cif.gz | 150 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a9n.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 8a9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a9n ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a9n | HTTPS FTP |
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-Related structure data
Related structure data | 8a9oC 6gtpS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18337.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: Aba9201_01540, ABR2091_2278, ABUW_1603, ACX61_07190, APC21_20150, APD31_09770, AYR68_11090, B7L45_07990, BAA1790NC_2350, BAA1790NC_2370, BS065_06845, C2U32_07150, C6N18_11935, CBL15_06645, ...Gene: Aba9201_01540, ABR2091_2278, ABUW_1603, ACX61_07190, APC21_20150, APD31_09770, AYR68_11090, B7L45_07990, BAA1790NC_2350, BAA1790NC_2370, BS065_06845, C2U32_07150, C6N18_11935, CBL15_06645, CPI82_05975, CSB70_2184, CTZ19_07130, D8O08_013765, DLI71_04685, DLI72_12170, DVA69_08365, E1A87_13275, E2532_16715, E2533_09885, E2534_09490, E2535_09465, E2536_09480, E2538_08415, E2539_09380, E2540_11625, E2541_08395, EA686_20485, EA720_017220, EA722_17035, EGM95_07835, EKS29_07930, EWO96_04140, F2P40_03430, F4T85_15855, FDN00_08240, FE003_07065, FGL68_01250, FJU42_16945, FJU76_02830, GNY86_02530, GSE42_12350, H0529_02675, H1058_07095, HB367_07820, HBK86_10405, IAG11_07575, IMO23_11370, ITE13_15710, NCTC13305_03823, NCTC13421_01499, SAMEA104305318_03080, SAMEA104305340_02732, SAMEA104305385_00035, SI89_01875 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: V5VBK4 |
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-Non-polymers , 6 types, 243 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-LFU / ~{ | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-13D / | #7: 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: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 293.16 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000, 0.1 mM acetyl-CoA |
-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: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→41.66 Å / Num. obs: 25133 / % possible obs: 97.37 % / Redundancy: 4.6 % / Biso Wilson estimate: 38.49 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.054 / Net I/σ(I): 8.43 |
Reflection shell | Resolution: 1.85→1.97 Å / Num. unique obs: 2407 / CC1/2: 0.418 / Rpim(I) all: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GTP Resolution: 1.854→41.66 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.158
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Displacement parameters | Biso mean: 36.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.854→41.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.854→1.87 Å
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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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