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- PDB-8xjh: Crystal structure of Arabidopsis N-amino acetyltransferase 2 (AtN... -

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Basic information

Entry
Database: PDB / ID: 8xjh
TitleCrystal structure of Arabidopsis N-amino acetyltransferase 2 (AtNATA2) bound to di-CoA
ComponentsGCN5-related N-acetyltransferase 8
KeywordsTRANSFERASE
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
Chem-5NG / GCN5-related N-acetyltransferase 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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) bound to di-CoA
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
B: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3155
Polymers48,1572
Non-polymers3,1583
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-47 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.450, 85.550, 86.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24078.541 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000

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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: Nov 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.75→46.67 Å / Num. obs: 41905 / % possible obs: 99.94 % / Redundancy: 14.3 % / CC1/2: 0.99 / Net I/σ(I): 13.46
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 4113 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.67 Å / SU B: 6.774 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22604 2114 5 %RANDOM
Rwork0.18783 ---
obs0.18955 39791 99.91 %-
Displacement parametersBiso mean: 42.879 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-0 Å2-0 Å2
2---0.59 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 0 88 3522
LS refinement shellResolution: 1.75→1.81 Å /
Num. reflection% reflection
Rwork4113 -
obs-99.73 %

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