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- PDB-8a9n: Structure of DpA polyamine acetyltransferase in complex with 1,3-DAP -

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Basic information

Entry
Database: PDB / ID: 8a9n
TitleStructure of DpA polyamine acetyltransferase in complex with 1,3-DAP
ComponentsAcetyltransferase
KeywordsTRANSFERASE / polyamine acetyltransferase / GNAT / bacterial biofilm formation / Acinetorbacter baumannii
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding / membrane
Similarity search - Function
Acetyltransferase, GNAT, predicted / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3-DIAMINOPROPANE / COENZYME A / ~{N}-(3-azanylpropyl)ethanamide / Acetyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsGarcia-Pino, A. / Jurenas, D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)T.0090.22 Belgium
CitationJournal: 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
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase
B: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5429
Polymers36,6762
Non-polymers1,8667
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-55 kcal/mol
Surface area13800 Å2
Unit cell
Length a, b, c (Å)42.870, 68.080, 55.740
Angle α, β, γ (deg.)90.00, 109.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetyltransferase / Acetyltransferase (GNAT) family protein / Acetyltransferase domain protein / Acetyltransferase / ...Acetyltransferase (GNAT) family protein / Acetyltransferase domain protein / Acetyltransferase / GNAT family / GNAT family N-acetyltransferase / N-acetyltransferase / Putative acetyltransferase


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 ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-LFU / ~{N}-(3-azanylpropyl)ethanamide


Mass: 116.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-13D / 1,3-DIAMINOPROPANE


Mass: 74.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H10N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.85→1.97 Å / Num. unique obs: 2407 / CC1/2: 0.418 / Rpim(I) all: 0.67

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTP

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 1257 5 %RANDOM
Rwork0.2059 ---
obs0.2082 25133 97.6 %-
Displacement parametersBiso mean: 36.13 Å2
Baniso -1Baniso -2Baniso -3
1--6.9274 Å20 Å22.4858 Å2
2---4.8166 Å20 Å2
3---11.744 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.854→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 117 236 2819
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082717HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.953690HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d957SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes469HARMONIC5
X-RAY DIFFRACTIONt_it2717HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion16.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion344SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2555SEMIHARMONIC4
LS refinement shellResolution: 1.854→1.87 Å
RfactorNum. reflection% reflection
Rfree0.4292 -4.97 %
Rwork0.399 478 -
obs--83.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3649-0.07390.4050.62220.00742.11010.00790.02950.0423-0.0593-0.086-0.03970.09390.09590.0782-0.09320.0122-0.005-0.105-0.00230.0818-5.13445.295621.6224
20.88440.17650.03840.7772-0.24421.76460.0532-0.05680.04790.1198-0.07720.0307-0.0432-0.02360.024-0.0808-0.0145-0.0232-0.10850.00240.0659-5.12188.632647.386
3-0.23440.02890.15790.39930.95652.0845-0.0048-0.07780.0198-0.0189-0.054-0.11360.21640.26340.0588-0.04850.02330.0091-0.0167-0.00440.0944-1.6673-2.500235.8714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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