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- PDB-8xjf: Crystal structure of Arabidopsis N-amino acetyltransferase 2 boun... -

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Basic information

Entry
Database: PDB / ID: 8xjf
TitleCrystal structure of Arabidopsis N-amino acetyltransferase 2 bound to HEPES, Acetyl CoA, GABA, and glycerol
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
GAMMA-AMINO-BUTANOIC ACID / ACETYL COENZYME *A / GCN5-related N-acetyltransferase 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 bound to HEPES, Acetyl CoA, GABA, and glycerol
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)25,3225
Polymers24,0791
Non-polymers1,2434
Water66737
1
A: GCN5-related N-acetyltransferase 8
hetero molecules

A: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,64310
Polymers48,1572
Non-polymers2,4868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area12560 Å2
ΔGint-27 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.060, 69.740, 104.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 41 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: 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
#4: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH 7.5, and 30% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→45.55 Å / Num. obs: 14957 / % possible obs: 99.2 % / Redundancy: 10.6 % / CC1/2: 0.99 / Net I/σ(I): 6.2
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1088 / CC1/2: 0.37

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.55 Å / SU B: 11.352 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23258 1502 10 %RANDOM
Rwork0.18552 ---
obs0.19008 13513 99.17 %-
Displacement parametersBiso mean: 55.545 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 79 37 1780
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.52 136 10 %
Rwork0.46 1352 -
obs--91.79 %

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