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- PDB-8a9o: Structure of the polyamine acetyltransferase DpA -

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Basic information

Entry
Database: PDB / ID: 8a9o
TitleStructure of the polyamine acetyltransferase DpA
ComponentsDpA polyamine acetyltransferase
KeywordsTRANSFERASE / 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
Acetyltransferase, GNAT, predicted / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / BROMIDE ION / COENZYME A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.587 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DpA polyamine acetyltransferase
B: DpA polyamine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,81826
Polymers36,7082
Non-polymers3,11024
Water5,495305
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-75 kcal/mol
Surface area14220 Å2
Unit cell
Length a, b, c (Å)43.330, 69.295, 55.773
Angle α, β, γ (deg.)90.00, 109.08, 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 DpA polyamine acetyltransferase


Mass: 18353.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A385EXR5

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Non-polymers , 6 types, 329 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293.16 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98015 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98015 Å / Relative weight: 1
ReflectionResolution: 1.587→69.3 Å / Num. obs: 37959 / % possible obs: 90.07 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.033 / Net I/σ(I): 14.55
Reflection shellResolution: 1.587→1.593 Å / Num. unique obs: 2163 / CC1/2: 0.695 / Rpim(I) all: 0.394

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.587→21.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1866 4.92 %RANDOM
Rwork0.189 ---
obs0.1906 37956 90 %-
Displacement parametersBiso mean: 24.98 Å2
Baniso -1Baniso -2Baniso -3
1--5.5334 Å20 Å2-0.2775 Å2
2--1.9189 Å20 Å2
3---3.6145 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.587→21.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 121 306 2884
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082691HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933668HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d968SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes488HARMONIC5
X-RAY DIFFRACTIONt_it2588HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion15.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion347SEMIHARMONIC5
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_contact2506SEMIHARMONIC4
LS refinement shellResolution: 1.59→1.61 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2797 -3.82 %
Rwork0.2903 731 -
all0.2898 760 -
obs--46.84 %
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)
10.4129-0.0539-0.22550.2465-0.21741.49120.00950.0166-0.0223-0.0372-0.02050.0003-0.00590.05870.0110.0005-0.00730.0108-0.0474-0.0095-0.0241-4.82414.099921.3689
20.47890.1955-0.06090.30080.0691.3203-0.0352-0.0539-0.00260.0087-0.01220.0007-0.05120.01590.0475-0.01450.011-0.0102-0.0250.014-0.0235-4.8197.023348.0577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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