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- PDB-9emo: Crystal structure of Histidine acetyltransferase with L-arginine ... -

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Basic information

Entry
Database: PDB / ID: 9emo
TitleCrystal structure of Histidine acetyltransferase with L-arginine 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 / ARGININE / Probable N-acetyltransferase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 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

Downloads & links

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Assembly

Deposited unit
A: Probable N-acetyltransferase 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9524
Polymers37,1521
Non-polymers1,8003
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-1 kcal/mol
Surface area14570 Å2
Unit cell
Length a, b, c (Å)90.965, 90.965, 99.379
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

#1: Protein Probable N-acetyltransferase 16


Mass: 37151.543 Da / Num. of mol.: 1 / Mutation: Residues 5-45 deleted
Source method: isolated from a genetically manipulated source
Details: Residues 5-45 deleted. C-terminal 6xHis tag. / 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
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, L-Arginine, 0.7 mM Ac-CoA. Well solution: 0.1 M Bis-tris pH 6.8, 20% PEG 3350. Cryo solution: 0.1 M Bis-tris pH 6.8, 20% PEG ...Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, L-Arginine, 0.7 mM Ac-CoA. Well solution: 0.1 M Bis-tris pH 6.8, 20% PEG 3350. Cryo solution: 0.1 M Bis-tris pH 6.8, 20% PEG 3350, 20% Glycerol, 1 mM L-Arginine, 1 mM Ac-CoA
PH range: 6.8-7.5

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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 PILATUS 6M-F / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→78.8 Å / Num. obs: 72335 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 41.4 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.122 / Net I/σ(I): 7.51
Reflection shellResolution: 1.9→2.02 Å / Mean I/σ(I) obs: 0.39 / Num. unique obs: 11720 / CC1/2: 0.178 / Rrim(I) all: 4.06

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 31, 2020data reduction
XDSJan 31, 2020data scaling
PHASER2.8.3phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.48 Å / SU ML: 0.3796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2385 3464 4.99 %
Rwork0.2225 65975 -
obs0.2233 69439 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 114 149 2802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752710
X-RAY DIFFRACTIONf_angle_d0.71163693
X-RAY DIFFRACTIONf_chiral_restr0.046405
X-RAY DIFFRACTIONf_plane_restr0.0052468
X-RAY DIFFRACTIONf_dihedral_angle_d12.5066419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.5021060.52742105X-RAY DIFFRACTION77.12
1.93-1.960.593640.59661370X-RAY DIFFRACTION49.48
1.96-1.990.45061340.47592490X-RAY DIFFRACTION89.8
1.99-2.020.46851380.45092578X-RAY DIFFRACTION95.1
2.02-2.050.46831460.42432680X-RAY DIFFRACTION98.02
2.05-2.090.38981410.37652676X-RAY DIFFRACTION99.26
2.09-2.120.38571450.36282748X-RAY DIFFRACTION99.83
2.12-2.160.30041470.34362791X-RAY DIFFRACTION99.83
2.16-2.210.34761450.32212756X-RAY DIFFRACTION99.83
2.21-2.260.33961380.3392693X-RAY DIFFRACTION100
2.26-2.310.32421490.28982742X-RAY DIFFRACTION99.93
2.31-2.370.34661450.28742747X-RAY DIFFRACTION100
2.37-2.430.28121420.26212737X-RAY DIFFRACTION99.97
2.43-2.50.29421460.24712738X-RAY DIFFRACTION99.69
2.5-2.580.29741440.23422744X-RAY DIFFRACTION100
2.58-2.670.28551480.22712737X-RAY DIFFRACTION100
2.67-2.780.25241440.22312714X-RAY DIFFRACTION100
2.78-2.910.29411450.23622777X-RAY DIFFRACTION100
2.91-3.060.26781390.22172737X-RAY DIFFRACTION99.69
3.06-3.250.2191380.20792738X-RAY DIFFRACTION99.58
3.25-3.50.19231420.19622725X-RAY DIFFRACTION100
3.5-3.860.25161440.18492755X-RAY DIFFRACTION100
3.86-4.410.17611440.16372721X-RAY DIFFRACTION99.62
4.42-5.560.14891430.17062735X-RAY DIFFRACTION99.41
5.56-45.480.19291470.19392741X-RAY DIFFRACTION99.55
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)
11.298853187930.114604443224-0.5660268593783.7626647172-0.9101809400723.42270959351-0.0299663928965-0.0104199484406-0.442404022124-0.3882203024120.0282001578299-0.1254546530280.3004246617910.00462420760613-0.01262942301270.322225302201-0.06154456247580.01898405534810.322530877555-0.04620527184620.64585558316820.69259742861.0716394237828.9544038256
24.28775048949-0.839445690655-2.800085936953.973451704262.674938777413.05703942207-0.130894964515-0.797860998215-0.0971609992820.2133205789070.481299179408-0.1087229683320.1796824807240.0768657562116-0.261716311280.338028264843-0.03830290459310.06534994172080.362514333013-0.04316308763880.57582591284133.338955724712.490419829331.0180115942
32.39156051944-0.446192074359-0.3340207708741.91955666857-0.01452809780561.91627900416-0.0938855416203-0.2125862008450.2029820112250.09453564492260.207498988866-0.139088993134-0.1876232621590.0244021586385-0.1204713021450.31365610155-0.00943791075699-0.00334643397220.316800862973-0.05495906151930.47939687437416.779336752126.430583567239.6839349331
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 47 through 150 )47 - 1501 - 104
22chain 'A' and (resid 151 through 173 )151 - 173105 - 127
33chain 'A' and (resid 174 through 371 )174 - 371128 - 325

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