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- PDB-8xjb: Crystal structure of AtNATA2 bound to Spermine -

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Basic information

Entry
Database: PDB / ID: 8xjb
TitleCrystal structure of AtNATA2 bound to Spermine
ComponentsGCN5-related N-acetyltransferase 8
KeywordsTRANSFERASE / polyamine
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
SPERMINE / GCN5-related N-acetyltransferase 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 AtNATA2 bound to Spermine
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,2812
Polymers24,0791
Non-polymers2021
Water2,504139
1
A: GCN5-related N-acetyltransferase 8
hetero molecules

A: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5624
Polymers48,1572
Non-polymers4052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area7340 Å2
ΔGint-51 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.730, 54.890, 51.910
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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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-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 40.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, and 25% 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: 1.448→34.93 Å / Num. obs: 33619 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 13.91
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 3139 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487-000)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→34.93 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 1999 5.95 %
Rwork0.151 --
obs0.154 33619 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 14 139 1802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051743
X-RAY DIFFRACTIONf_angle_d0.8332364
X-RAY DIFFRACTIONf_dihedral_angle_d5.396631
X-RAY DIFFRACTIONf_chiral_restr0.077257
X-RAY DIFFRACTIONf_plane_restr0.006302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48390.41981300.35382061X-RAY DIFFRACTION90
1.4839-1.5240.2921410.26792234X-RAY DIFFRACTION100
1.524-1.56880.30961430.2452253X-RAY DIFFRACTION100
1.5688-1.61950.32711430.22662265X-RAY DIFFRACTION100
1.6195-1.67730.30961450.21672282X-RAY DIFFRACTION100
1.6773-1.74450.22121400.1692220X-RAY DIFFRACTION100
1.7445-1.82390.23161440.13612274X-RAY DIFFRACTION100
1.8239-1.920.21181460.1282307X-RAY DIFFRACTION100
1.92-2.04030.18581430.12382260X-RAY DIFFRACTION100
2.0403-2.19780.18911440.12372281X-RAY DIFFRACTION100
2.1978-2.4190.20511440.13032278X-RAY DIFFRACTION100
2.419-2.76890.20891440.14382262X-RAY DIFFRACTION100
2.7689-3.4880.17081450.14672299X-RAY DIFFRACTION100
3.488-34.9290.14781470.15672344X-RAY DIFFRACTION100

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