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- PDB-9emt: Crystal structure of Histidine acetyltransferase with imidazole a... -

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Basic information

Entry
Database: PDB / ID: 9emt
TitleCrystal structure of Histidine acetyltransferase with imidazole and coenzyme A disulfide
ComponentsProbable N-acetyltransferase 16
KeywordsTRANSFERASE / Acyltransferase / GNAT fold
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
: / Histidine N-acetyltransferase, C-terminal / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Chem-5NG / IMIDAZOLE / MALONATE ION / Probable N-acetyltransferase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMyllykoski, M. / Arnesen, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)772039European Union
CitationJournal: Nat Commun / Year: 2025
Title: The molecular basis for acetylhistidine synthesis by HisAT/NAT16.
Authors: Myllykoski, M. / Lundekvam, M. / Osberg, C. / Nilsen, S.S. / Arnesen, T.
History
DepositionMar 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 16, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable N-acetyltransferase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0197
Polymers39,0381
Non-polymers1,9806
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint6 kcal/mol
Surface area14930 Å2
Unit cell
Length a, b, c (Å)91.129, 91.129, 98.487
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable N-acetyltransferase 16


Mass: 39038.461 Da / Num. of mol.: 1 / Mutation: Residues 5-27 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAT16, C7orf52 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8N8M0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 431 molecules

#2: Chemical ChemComp-5NG / [[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyldisulfanyl]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate / CoA-disulfide


Mass: 1533.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 2 mM adenosine, 1 mM Ac-CoA. Well solution: 0.1 M MIB buffer pH 6.5, 20% PEG3350. Cryo-solution: 75% well solution, 25% glycerol
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→41.8 Å / Num. obs: 90984 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 1 / Rrim(I) all: 0.048 / Net I/σ(I): 21.65
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 9 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 14572 / CC1/2: 0.326 / Rrim(I) all: 3.14 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
PHASER2.8.3phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→41.78 Å / SU ML: 0.194 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.1924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1795 2275 2.5 %
Rwork0.1603 88687 -
obs0.1607 90962 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 126 425 3090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382864
X-RAY DIFFRACTIONf_angle_d0.83913918
X-RAY DIFFRACTIONf_chiral_restr0.0616418
X-RAY DIFFRACTIONf_plane_restr0.0179488
X-RAY DIFFRACTIONf_dihedral_angle_d16.5395489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.38371390.41765435X-RAY DIFFRACTION98.72
1.43-1.460.40771420.36565525X-RAY DIFFRACTION99.91
1.46-1.50.34061420.33125524X-RAY DIFFRACTION99.95
1.5-1.540.28131420.2645543X-RAY DIFFRACTION99.96
1.54-1.590.25271410.21885513X-RAY DIFFRACTION99.96
1.59-1.640.22391430.17815559X-RAY DIFFRACTION99.91
1.64-1.70.20591420.15745532X-RAY DIFFRACTION99.95
1.7-1.760.17261420.14475540X-RAY DIFFRACTION99.96
1.76-1.840.17961410.14475517X-RAY DIFFRACTION99.96
1.84-1.940.17471430.14725568X-RAY DIFFRACTION99.96
1.94-2.060.17051420.14175549X-RAY DIFFRACTION99.96
2.06-2.220.20471420.14125533X-RAY DIFFRACTION99.93
2.22-2.450.14621430.13945558X-RAY DIFFRACTION100
2.45-2.80.17981430.1455578X-RAY DIFFRACTION99.97
2.8-3.530.17091430.15585573X-RAY DIFFRACTION100
3.53-41.780.16531450.16135640X-RAY DIFFRACTION99.88

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