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- PDB-8xj9: Crystal Structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2) -

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Basic information

Entry
Database: PDB / ID: 8xj9
TitleCrystal Structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2)
ComponentsGCN5-related N-acetyltransferase 8
KeywordsTRANSFERASE / Acetyltransferase / polyamine acetylation
Function / homology
Function and homology information


protein-N-terminal amino-acid acetyltransferase activity / N-acetyltransferase activity / protein-lysine-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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / GCN5-related N-acetyltransferase 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKIng Abdullah University of Science and Technology Saudi Arabia
CitationJournal: To Be Published
Title: Crystal Structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2)
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionDec 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3353
Polymers24,0791
Non-polymers2562
Water2,414134
1
A: GCN5-related N-acetyltransferase 8
hetero molecules

A: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6706
Polymers48,1572
Non-polymers5134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7750 Å2
ΔGint-41 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.700, 54.840, 51.700
Angle α, β, γ (deg.)90.00, 113.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GCN5-related N-acetyltransferase 8 / Probable acetyltransferase NATA1-like


Mass: 24078.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GNAT8
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9ZV06, histone acetyltransferase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.1→47.27 Å / Num. obs: 75934 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 8.3
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3489 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→36.64 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.81 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19549 2000 2.6 %RANDOM
Rwork0.15301 ---
obs0.1541 73933 99.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20.05 Å2
2---0.53 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.1→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 17 134 1800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0171749
X-RAY DIFFRACTIONr_bond_other_d0.0020.0191630
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.8472378
X-RAY DIFFRACTIONr_angle_other_deg1.2672.673750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.20120.75393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76415277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.031513
X-RAY DIFFRACTIONr_chiral_restr0.1380.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9581.841844
X-RAY DIFFRACTIONr_mcbond_other1.8081.84843
X-RAY DIFFRACTIONr_mcangle_it2.2922.771062
X-RAY DIFFRACTIONr_mcangle_other2.3352.7711063
X-RAY DIFFRACTIONr_scbond_it2.6912.204905
X-RAY DIFFRACTIONr_scbond_other2.692.207906
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1393.1831317
X-RAY DIFFRACTIONr_long_range_B_refined3.35722.2071910
X-RAY DIFFRACTIONr_long_range_B_other3.23621.9211888
X-RAY DIFFRACTIONr_rigid_bond_restr2.97533379
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.61 139 -
Rwork0.609 5125 -
obs--93.95 %

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