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- PDB-7ovv: Crystal structure of the Arabidopsis thaliana thialysine acetyltr... -

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Basic information

Entry
Database: PDB / ID: 7ovv
TitleCrystal structure of the Arabidopsis thaliana thialysine acetyltransferase AtNATA2
ComponentsProbable acetyltransferase NATA1-like
KeywordsPLANT PROTEIN / GNAT N-acetyltransferase thialysine acetyl coenzyme A
Function / homology
Function and homology information


N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / histone acetyltransferase / nucleus / cytosol
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Chem-5NG / GCN5-related N-acetyltransferase 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLayer, D. / Kopp, J. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1036 (TP22) Germany
German Research Foundation (DFG)Leibniz program (SI 586/6-1) Germany
CitationJournal: To Be Published
Title: Structural insights into the Arabidopsis thaliana thialysine acetyltransferase AtNATA2
Authors: Layer, D. / Stier, G. / Kopp, J. / Sinning, I.
History
DepositionJun 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable acetyltransferase NATA1-like
B: Probable acetyltransferase NATA1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7974
Polymers45,7312
Non-polymers3,0662
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS measurments confirm that AtNATA2 is a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-37 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.766, 104.388, 51.786
Angle α, β, γ (deg.)90.000, 108.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable acetyltransferase NATA1-like


Mass: 22865.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g39020, T7F6.19 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9ZV06, 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.: 2 / Source method: obtained synthetically / Formula: C42H70N14O32P6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: AtNATA229-226 was concentrated to 10 mg/ml and incubated with a fivefold molar excess of CoA for 18 h on ice. Crystallization drops contained 200 nl protein solution and 200 nl precipitant ...Details: AtNATA229-226 was concentrated to 10 mg/ml and incubated with a fivefold molar excess of CoA for 18 h on ice. Crystallization drops contained 200 nl protein solution and 200 nl precipitant solution. Crystals appeared within 2-18 hours in several conditions. The best diffracting crystals were obtained from the precipitant condition with 0.1 M sodium citrate (pH 5.5), 0.2 M lithium sulfate and 15 % (v/v) ethanol. Crystals were cryo-protected with 20 % glycerol and flash-frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972423 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972423 Å / Relative weight: 1
ReflectionResolution: 1.45→49.24 Å / Num. obs: 70882 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 11.5 / Num. measured all: 435296 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.471.5282210235540.6040.6621.6691.299.9
7.94-49.240.03827864470.9970.0160.04240.699.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fe7

2fe7


Resolution: 1.45→44.54 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 3463 4.89 %
Rwork0.1552 67345 -
obs0.1569 70808 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.63 Å2 / Biso mean: 37.1394 Å2 / Biso min: 12.34 Å2
Refinement stepCycle: final / Resolution: 1.45→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 316 272 3754
Biso mean--67.56 39.12 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.470.33581280.303727432871100
1.47-1.490.33561210.280526672788100
1.49-1.510.28351430.26727052848100
1.51-1.540.27621310.262826512782100
1.54-1.560.30961390.233527312870100
1.56-1.590.26941410.218926782819100
1.59-1.620.25791610.198626882849100
1.62-1.650.2261330.180326712804100
1.65-1.680.22851370.170826852822100
1.68-1.720.21341290.166827062835100
1.72-1.760.21771410.170126782819100
1.76-1.80.24461570.173626942851100
1.8-1.850.20611250.161526772802100
1.85-1.910.21481220.150327302852100
1.91-1.970.16851140.138227182832100
1.97-2.040.19111420.128426572799100
2.04-2.120.18131460.140327092855100
2.12-2.220.19381340.142726972831100
2.22-2.330.18621630.138126802843100
2.33-2.480.16561590.139327122871100
2.48-2.670.17981320.150826902822100
2.67-2.940.18221380.15242668280699
2.94-3.360.18461220.14842733285599
3.36-4.240.17151590.14052656281599
4.24-44.540.15581460.15442721286799

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