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- PDB-7ovu: Crystal structure of Arabidopsis thaliana NAT9 in complex with AcCoA -

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Basic information

Entry
Database: PDB / ID: 7ovu
TitleCrystal structure of Arabidopsis thaliana NAT9 in complex with AcCoA
ComponentsAcyl-CoA N-acyltransferases (NAT) superfamily protein
KeywordsPLANT PROTEIN / GNAT N-acetyltransferase AcCoA PLANT PROTEIN NAT9
Function / homology
Function and homology information


N-acetyltransferase activity / histone acetyltransferase / nucleus / cytosol
Similarity search - Function
N-acetyltransferase 9-like / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / GCN5-related N-acetyltransferase 9
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLayer, D. / Weyer, F.A. / 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: Crystal structure of the Arabidopsis thaliana N-acetyltransferase 9
Authors: Layer, D. / Weyer, F.A. / 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

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Assembly

Deposited unit
A: Acyl-CoA N-acyltransferases (NAT) superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3712
Polymers24,5611
Non-polymers8101
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALS measurments confirm that AtNAT9 is a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area10180 Å2
Unit cell
Length a, b, c (Å)67.202, 48.895, 60.123
Angle α, β, γ (deg.)90.000, 102.750, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

21A-529-

HOH

31A-553-

HOH

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Components

#1: Protein Acyl-CoA N-acyltransferases (NAT) superfamily protein / Expressed protein


Mass: 24560.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g04845 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8S8E7
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: AtNAT9 was concentrated to 15 mg/ml and incubated with a threefold molar excess of AcCoA for 18 h on ice. Crystallization drops contained 200 nl protein solution and 200 nl precipitant ...Details: AtNAT9 was concentrated to 15 mg/ml and incubated with a threefold molar excess of AcCoA for 18 h on ice. Crystallization drops contained 200 nl protein solution and 200 nl precipitant solution (0.1 M HEPES (pH 7) and 20 % PEG6000) and crystals appeared after seven days. The 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: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.45→39.19 Å / Num. obs: 33777 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.9
Reflection shellResolution: 1.45→1.5 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3306 / CC1/2: 0.509

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eo4

3eo4


Resolution: 1.45→39.19 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1809 1673 4.96 %
Rwork0.1486 32084 -
obs0.1502 33757 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.41 Å2 / Biso mean: 30.7526 Å2 / Biso min: 15.05 Å2
Refinement stepCycle: final / Resolution: 1.45→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 51 153 1771
Biso mean--38.12 36.1 -
Num. residues----196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.490.30111350.23772625276097
1.49-1.540.26581400.21326702810100
1.54-1.60.25441370.197326382775100
1.6-1.660.22351230.180526762799100
1.66-1.740.20791260.158526722798100
1.74-1.830.20661470.140726642811100
1.83-1.940.17211420.132826652807100
1.94-2.090.18541390.131526792818100
2.09-2.30.16731400.126626922832100
2.3-2.630.17781550.142326522807100
2.63-3.320.15531400.152426962836100
3.32-39.190.17571490.147327552904100

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