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- PDB-9emp: Crystal structure of Histidine acetyltransferase with N-myristoyl... -

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Basic information

Entry
Database: PDB / ID: 9emp
TitleCrystal structure of Histidine acetyltransferase with N-myristoyl histidine and 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
: / COENZYME A / Probable N-acetyltransferase 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 9, 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)38,4695
Polymers37,1521
Non-polymers1,3174
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-0 kcal/mol
Surface area15410 Å2
Unit cell
Length a, b, c (Å)49.929, 111.853, 156.855
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

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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-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-A1H51 / (2~{S})-3-(1~{H}-imidazol-5-yl)-2-(tetradecanoylamino)propanoic acid


Mass: 365.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H35N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.9 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Protein buffer: 10 mM Tris-HCl pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM L-Histidine, 0.7 mM Myr-CoA. Well solution: 0.1 M Bis-tris pH 6.8, 22% PEG3350. 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, 1 mM L-Histidine, 0.7 mM Myr-CoA. Well solution: 0.1 M Bis-tris pH 6.8, 22% PEG3350. Cryo solution: 0.1 M Bis-tris pH 6.8, 22% PEG3350, 20% Glycerol
PH range: pH 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: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.45→91.1 Å / Num. obs: 75754 / % possible obs: 96.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 1 / Rrim(I) all: 0.057 / Net I/σ(I): 16.41
Reflection shellResolution: 1.45→1.54 Å / Mean I/σ(I) obs: 0.69 / Num. unique obs: 11509 / CC1/2: 0.505 / Rrim(I) all: 2.67 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSJan 31, 2020data reduction
XDSJan 31, 2020data scaling
PHASER2.8.3phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→47.37 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.4948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 2267 3 %
Rwork0.1879 73244 -
obs0.1885 75511 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.58 Å2
Refinement stepCycle: LAST / Resolution: 1.45→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 86 313 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892776
X-RAY DIFFRACTIONf_angle_d1.06833776
X-RAY DIFFRACTIONf_chiral_restr0.0819413
X-RAY DIFFRACTIONf_plane_restr0.0102487
X-RAY DIFFRACTIONf_dihedral_angle_d13.7156422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.69971250.64613988X-RAY DIFFRACTION85.17
1.48-1.510.5641360.55864435X-RAY DIFFRACTION93.92
1.51-1.550.56541400.48054483X-RAY DIFFRACTION95.77
1.55-1.590.51351380.46954487X-RAY DIFFRACTION95.42
1.59-1.640.37611390.42024502X-RAY DIFFRACTION95.51
1.64-1.690.42481410.35764540X-RAY DIFFRACTION96.14
1.69-1.750.32031390.28314536X-RAY DIFFRACTION96.37
1.75-1.820.29391420.23334565X-RAY DIFFRACTION96.77
1.82-1.910.22891420.21664596X-RAY DIFFRACTION96.95
1.91-2.010.25351430.20434619X-RAY DIFFRACTION97.42
2.01-2.130.18491440.1654650X-RAY DIFFRACTION98.14
2.13-2.30.16231440.15244637X-RAY DIFFRACTION97.51
2.3-2.530.17151450.15094692X-RAY DIFFRACTION98.33
2.53-2.90.18541470.16124746X-RAY DIFFRACTION98.89
2.9-3.650.17391480.15794781X-RAY DIFFRACTION98.84
3.65-47.370.1731540.15774987X-RAY DIFFRACTION99.04
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)
10.779663492437-0.2379553704030.5564908139443.06032900084-3.13405352163.32593601762-0.115961541105-0.3567460606920.4190425526890.4780804265490.7239401462420.4021947722741.10307375689-1.11560847499-0.5671741504880.7478296297250.00779074378549-0.01858263727330.6402378759890.04262333380340.447252072568-29.4009334435-47.438661114-3.08396151728
26.0328300895-4.22590794165-3.034372720276.726786287543.3538020315.45645810506-0.01600210731250.0109638969879-0.1018685453360.0897015538981-0.0165794339565-0.08292276569920.371800798209-0.2626682789480.006901627136180.308174216085-0.0366753026024-0.02688757186770.3154270654970.07013500936120.326080900178-27.1660152659-33.8034777089-27.1932772053
36.03678340255-0.0514895717328-0.9393932348132.093422296410.3990477705861.7082853050.18145075926-0.368478871446-0.2989576352320.156793039445-0.151477922766-0.1488018350540.19448095547-0.148600242345-0.02282112454440.399498286462-0.0602756675002-0.05790182824870.411665510540.1418154570980.380550568787-22.7753462697-37.4385598323-18.4000940972
49.60148983125-6.39222574304-2.037925251478.746982454470.9108137925974.36793367156-0.100195823933-0.776223061014-0.5674391132560.785283526265-0.149069597136-0.4905520067090.274275297541-0.1830078786290.2570748613020.580896916915-0.12607832974-0.1659125921650.5002497597090.190924390840.471131531072-20.6887507631-41.5097877475-11.5931138371
52.87529565086-1.697185711251.242429347655.08023117575-1.83568646772.3955743607-0.148805157467-0.822634079687-0.3848802381941.008190542340.2608031583870.118249104037-0.147537501488-0.115001381212-0.141720426010.474174822887-0.00556685737638-0.01138397464760.5166964025230.08808308336780.334926570945-14.8348591013-22.8245800046-14.262063433
62.96045579375-2.66260654474-0.5764555494292.910804061190.5629605312820.1169945310080.1070763360770.0366303285090.25369952348-0.167643836965-0.0517122733178-0.3467232549520.010505687763-0.0135748835865-0.06546608090910.3501541957120.004449314635190.01381027761810.3359548664750.02624215980480.349681081993-12.3710722994-1.90376246167-37.8243846935
72.503729234340.147982603604-1.070040650041.6998278576-0.1612542829991.471129777010.0459333404034-0.258219853266-0.339395813580.127051664188-0.0331464836895-0.2693130599050.1212156656140.139474726302-0.03053744312260.34770765702-0.00894960487744-0.07440862517280.3671257097190.07184673350940.431591422366-2.64724392361-25.7180113466-27.6676827941
82.565349589020.996765320422-0.2381292953182.35907306064-0.1315793131180.219905619075-0.0259605458201-0.1418852476690.0860629640981-0.00792856237636-0.03412246984570.000339174889056-0.0494219120813-0.02058719032920.07652861524750.325810582705-0.00258638430366-0.0438243831580.3408270692160.01319770647010.331721745678-13.2164612813-17.4788474868-31.5109028003
93.36681345117-0.723954899818-0.6220705770832.30570619041-0.1249506136710.9558471559750.0475616621656-0.09777918043350.1613830861080.06799761798930.0164611470302-0.0572331763854-0.0733505939612-0.0361024057085-0.06219492275040.303467602751-0.00720770680973-0.03831761471350.2885817482170.01457415458680.335479400174-14.9554694986-9.37388972745-30.5805691068
104.79855255584-3.632931788352.210019861956.68183873749-2.423577855693.19512134225-0.212659624981-0.805182546681-0.4333060246430.8718870726620.3767155474020.154391526006-0.0291698371437-0.132099517377-0.1962267093110.36546752888-0.0185786098585-0.01765675931490.4579954751440.0661104468780.289312140172-15.2906403632-21.2513861661-15.006284656
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 58 )42 - 581 - 17
22chain 'A' and (resid 59 through 91 )59 - 9118 - 50
33chain 'A' and (resid 92 through 130 )92 - 13051 - 89
44chain 'A' and (resid 131 through 152 )131 - 15290 - 111
55chain 'A' and (resid 153 through 188 )153 - 188112 - 147
66chain 'A' and (resid 189 through 217 )189 - 217148 - 176
77chain 'A' and (resid 218 through 263 )218 - 263177 - 222
88chain 'A' and (resid 264 through 304 )264 - 304223 - 263
99chain 'A' and (resid 305 through 352 )305 - 352264 - 311
1010chain 'A' and (resid 353 through 371 )353 - 371312 - 330

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