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- PDB-9en3: Crystal structure of Histidine acetyltransferase with L-histidine... -

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Basic information

Entry
Database: PDB / ID: 9en3
TitleCrystal structure of Histidine acetyltransferase with L-histidine and S-ethyl-coenzyme A
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
: / HISTIDINE / 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: To Be Published
Title: Human NAT16 encodes histidine alpha-acetyltransferase
Authors: Myllykoski, M. / Osberg, C. / Lundekvam, M. / Arnesen, T.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 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)38,5999
Polymers37,1521
Non-polymers1,4488
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.798, 110.824, 153.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable N-acetyltransferase 16


Mass: 37151.543 Da / Num. of mol.: 1 / Mutation: residues 5-45 were deleted
Source method: isolated from a genetically manipulated source
Details: This construct has residues 5-45 of NAT16 sequence deleted and a 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 , 5 types, 405 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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
#4: Chemical ChemComp-A2U / S-Ethyl-CoA


Mass: 795.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H40N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 0.7 mM S-Ethyl-CoA, 0.7 mM L-Histidine. Well solution: 0.1 M HEPES pH 7, 18% PEG 3000. Cryo-solution: 0.1 M Bis-tris pH 6.8, ...Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 0.7 mM S-Ethyl-CoA, 0.7 mM L-Histidine. Well solution: 0.1 M HEPES pH 7, 18% PEG 3000. Cryo-solution: 0.1 M Bis-tris pH 6.8, 20% PEG 3000, 25% glycerol, 1 mM S-Ethyl-CoA, 0.7 mM L-Histidine
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, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.4→46.5341 Å / Num. obs: 160267 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.056 / Net I/σ(I): 11.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 25132 / CC1/2: 0.629 / Rrim(I) all: 1.41 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHASER2.8.3phasing
CootWinCoot 0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.53 Å / SU ML: 0.2175 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 27.8624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1825 8032 5.02 %
Rwork0.1656 152017 -
obs0.1664 160049 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 92 397 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782799
X-RAY DIFFRACTIONf_angle_d1.07963812
X-RAY DIFFRACTIONf_chiral_restr0.0793419
X-RAY DIFFRACTIONf_plane_restr0.0183496
X-RAY DIFFRACTIONf_dihedral_angle_d9.317425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.59422350.54884493X-RAY DIFFRACTION88.23
1.42-1.430.57912510.50674822X-RAY DIFFRACTION93.25
1.43-1.450.47222640.46955015X-RAY DIFFRACTION98.09
1.45-1.470.43242720.41315107X-RAY DIFFRACTION99.01
1.47-1.490.40332710.38535106X-RAY DIFFRACTION99.59
1.49-1.510.39842690.36755159X-RAY DIFFRACTION99.56
1.51-1.530.34142700.34735062X-RAY DIFFRACTION99.63
1.53-1.550.34022720.32845130X-RAY DIFFRACTION99.54
1.55-1.580.31222640.30595068X-RAY DIFFRACTION99.38
1.58-1.60.27732720.27415127X-RAY DIFFRACTION99.43
1.6-1.630.25262720.24715072X-RAY DIFFRACTION99.2
1.63-1.660.24682750.22425113X-RAY DIFFRACTION99.19
1.66-1.690.22362640.21035043X-RAY DIFFRACTION98.97
1.69-1.730.23152700.19335103X-RAY DIFFRACTION98.8
1.73-1.760.19912690.18865035X-RAY DIFFRACTION98.53
1.76-1.80.19562690.1675098X-RAY DIFFRACTION99.63
1.8-1.850.1972750.16885150X-RAY DIFFRACTION99.82
1.85-1.90.19452710.16055087X-RAY DIFFRACTION99.78
1.9-1.960.18822740.15325138X-RAY DIFFRACTION99.63
1.96-2.020.18542650.14135105X-RAY DIFFRACTION99.65
2.02-2.090.172700.13835135X-RAY DIFFRACTION99.67
2.09-2.170.16092660.13485104X-RAY DIFFRACTION99.3
2.17-2.270.15522700.13375088X-RAY DIFFRACTION99.08
2.27-2.390.13932650.13195058X-RAY DIFFRACTION98.67
2.39-2.540.15872590.13185010X-RAY DIFFRACTION98.14
2.54-2.740.14752750.13715154X-RAY DIFFRACTION99.93
2.74-3.010.15072730.14255116X-RAY DIFFRACTION99.91
3.02-3.450.15772710.13975135X-RAY DIFFRACTION99.74
3.45-4.350.1582670.13655086X-RAY DIFFRACTION99.26
4.35-46.530.16982720.17035098X-RAY DIFFRACTION98.8
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)
10.958299595343-0.5808820954360.1780380548931.76329359097-0.7441377793152.05993613620.000382334184286-0.297809657192-0.1600367264330.2376354034450.00745482795623-0.108609424790.227146914021-0.196935234450.004996661311640.245711915359-0.0554798071001-0.02843072761460.2498630310860.07026870401980.22634140943-24.9748615976-39.014045129-17.6269927449
22.66984325926-0.4673330912761.25678310414.10233057384-1.433869904475.18580769813-0.134093161405-0.777278375891-0.007469417517731.154642760880.168826840511-0.0249579531215-0.274431313656-0.299511594393-0.0325641380190.428745768489-0.0302669582777-0.04172724080080.4658485322230.1140167782670.332016171219-13.1559615612-30.3975314424-9.03552806743
31.70732280858-0.161069335765-0.06646349153881.39989081357-0.06352750150590.2243935377380.0117475301871-0.1749575741540.015720304440.0995888594376-0.0100470815418-0.060729978555-0.0145313809178-0.000409361465239-0.002162497544830.176298433514-0.006718633274-0.02546725692270.190925084581-0.007554263331290.172038668661-11.5454559165-15.489829923-27.606369782
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 42 through 150 )42 - 1501 - 109
22chain 'A' and (resid 151 through 173 )151 - 173110 - 132
33chain 'A' and (resid 174 through 370 )174 - 370133 - 329

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