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- PDB-9emd: Crystal structure of Histidine acetyltransferase with L-histidine... -

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Basic information

Entry
Database: PDB / ID: 9emd
TitleCrystal structure of Histidine acetyltransferase with L-histidine 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 / HISTIDINE / MALONATE ION / Probable N-acetyltransferase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsMyllykoski, M. / Arnesen, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)772039European Union
CitationJournal: To Be Published
Title: Human NAT16 encodes histidine alpha-acetyltransferase
Authors: Myllykoski, M. / Osberg, C. / Lundekvam, M. / Arnesen, T.
History
DepositionMar 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)41,2349
Polymers39,0381
Non-polymers2,1958
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-10 kcal/mol
Surface area14840 Å2
Unit cell
Length a, b, c (Å)90.495, 90.495, 98.634
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
Details: Residues 5-27 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

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Non-polymers , 6 types, 350 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.9 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Sample buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM L-Histidine, 0.7 mM CoA. Well buffer: 0.1 M MIB buffer pH 7.0, 25 % w/v PEG 1500. Cryo-solution: 60% well solution, 20% ...Details: Sample buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM L-Histidine, 0.7 mM CoA. Well buffer: 0.1 M MIB buffer pH 7.0, 25 % w/v PEG 1500. Cryo-solution: 60% well solution, 20% Glycerol, 20% PEG 1500
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→78.4 Å / Num. obs: 60369 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 1 / Rrim(I) all: 0.063 / Net I/σ(I): 21.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 9763 / CC1/2: 0.495 / Rrim(I) all: 3.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 31, 2020data reduction
SHELXE2019/1model building
XSCALEJan 31, 2020data scaling
SHELXCDC: 2016/1, D:2013/2phasing
PHENIX2.15model building
Cootmodel building
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→78.37 Å / SU ML: 0.2555 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1853 3017 5 %
Rwork0.1665 57332 -
obs0.1675 60349 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.52 Å2
Refinement stepCycle: LAST / Resolution: 1.6→78.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2539 0 139 342 3020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632805
X-RAY DIFFRACTIONf_angle_d0.99443825
X-RAY DIFFRACTIONf_chiral_restr0.0517412
X-RAY DIFFRACTIONf_plane_restr0.009491
X-RAY DIFFRACTIONf_dihedral_angle_d13.1155447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.47751360.4442598X-RAY DIFFRACTION99.82
1.62-1.650.4291380.38792624X-RAY DIFFRACTION100
1.65-1.680.35961370.34212594X-RAY DIFFRACTION99.96
1.68-1.710.29491350.29462586X-RAY DIFFRACTION99.93
1.71-1.740.26131360.25182591X-RAY DIFFRACTION99.93
1.74-1.780.23551370.23292596X-RAY DIFFRACTION99.6
1.78-1.820.28051350.22362571X-RAY DIFFRACTION99.96
1.82-1.860.24251390.21372624X-RAY DIFFRACTION99.96
1.86-1.910.23381360.21822599X-RAY DIFFRACTION100
1.91-1.960.27721370.21832591X-RAY DIFFRACTION99.82
1.96-2.020.21661370.18342615X-RAY DIFFRACTION99.96
2.02-2.080.20971370.16792596X-RAY DIFFRACTION100
2.08-2.150.17141380.16112627X-RAY DIFFRACTION100
2.16-2.240.18541360.15852584X-RAY DIFFRACTION99.96
2.24-2.340.20011370.1512601X-RAY DIFFRACTION100
2.34-2.470.19371370.15252606X-RAY DIFFRACTION99.75
2.47-2.620.18961370.1582594X-RAY DIFFRACTION100
2.62-2.820.18341380.15522618X-RAY DIFFRACTION99.89
2.82-3.110.1821370.15882616X-RAY DIFFRACTION100
3.11-3.560.16911380.15412619X-RAY DIFFRACTION100
3.56-4.480.15191390.142629X-RAY DIFFRACTION99.89
4.48-78.370.15981400.16122653X-RAY DIFFRACTION99.5
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)
11.916284652730.139700089457-0.1259927634455.21817575986-1.17803395842.28726112415-0.00969824024459-0.0139472176393-0.396231798577-0.260766434162-0.02312979953870.05274280772660.364007000836-0.08782257222690.01021440729990.262716216096-0.06800406094680.01205069898270.219980653502-0.03327535253130.28304258352617.97935894281.8030516398329.1707206433
23.850766960911.75093176997-2.045459825538.42207200776-6.745375397698.01007037006-0.0778233789165-0.128339266579-0.577582339789-0.392631171528-0.273652566495-0.4416004269670.6937977256130.3253940978590.3462370843860.244094140374-0.03463831695550.02066023820530.206456177102-0.02674327273930.40922486188527.1658997579-0.71068114905827.9497178564
37.51455209605-1.17090025968-2.789120737365.40264959764.893248708616.2255925081-0.31148879206-0.98089990944-0.1296564582350.4900722849750.474204230573-0.4000221932130.4898316365190.785141378839-0.1791479944580.3002701210350.04129861200760.04360656779840.297495689812-0.02626023122280.36695277834233.425180772212.361180590431.0267374118
44.5966059865-1.40606898096-2.327565466912.608313399480.6484218603172.63802993952-0.0097199746506-0.388857488040.1229943483910.4281855675640.1318013527930.0102199403806-0.425266022289-0.195789136255-0.163201375170.4015770975830.0545950457493-0.01214125788570.441232648827-0.05461065857210.18677179496914.049493509827.547857289949.4781430788
52.3443397003-0.690499472154-0.7779100302713.058069139090.08452340142182.453321354970.03958189631960.02248379046380.303401338030.009412954548330.00156491039453-0.0530995408535-0.213110999787-0.0867867143286-0.06991541925230.263856383321-0.02942511755620.01042363361140.248453345094-0.01550650412830.31791112835817.7447094431.282029891530.7028616314
62.8985506673-0.708765585483-0.6759038983681.456937608440.07215412486591.94479511494-0.13960751897-0.2754279818960.1191895035330.1975902433820.188429193197-0.115733099648-0.01224164055040.0136367477328-0.04545675058090.2550030543260.00198189811944-0.001317114177550.299392517069-0.0388821038560.22972233241116.855386447322.844047414642.9770621334
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 122 )47 - 1221 - 76
22chain 'A' and (resid 123 through 150 )123 - 15077 - 104
33chain 'A' and (resid 151 through 173 )151 - 173105 - 127
44chain 'A' and (resid 174 through 204 )174 - 204128 - 158
55chain 'A' and (resid 205 through 275 )205 - 275159 - 229
66chain 'A' and (resid 276 through 371 )276 - 371230 - 325

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