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- PDB-9s30: GnaT, N-acetyltransferase. -

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Basic information

Entry
Database: PDB / ID: 9s30
TitleGnaT, N-acetyltransferase.
ComponentsGNAT family N-acetyltransferase
KeywordsCYTOSOLIC PROTEIN / N-acetyltransferase
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / polyethylene glycol / GNAT family N-acetyltransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGarcia-Pino, A. / Talavera Perez, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)864311European Union
CitationJournal: To Be Published
Title: Structure of bacterial anti-phage defence system GNAT acetyltransferase
Authors: Garcia-Pino, A. / Talavera, A.
History
DepositionJul 23, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GNAT family N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5375
Polymers25,9481
Non-polymers1,5894
Water1,49583
1
A: GNAT family N-acetyltransferase
hetero molecules

A: GNAT family N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,07410
Polymers51,8972
Non-polymers3,1788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8050 Å2
ΔGint-74 kcal/mol
Surface area21120 Å2
Unit cell
Length a, b, c (Å)76.094, 126.811, 74.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GNAT family N-acetyltransferase


Mass: 25948.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GGB84_003431, NCTC8603_00132
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2Y8QZ56

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Non-polymers , 5 types, 87 molecules

#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: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: MIDAS C5: 5 % v/v pentaerythritol ethoxylate (3/4 EO/OH) 0.2 M Magnesium chloride

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.943204 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943204 Å / Relative weight: 1
ReflectionResolution: 2.65→48.28 Å / Num. obs: 20238 / % possible obs: 99.42 % / Redundancy: 5.5 % / Biso Wilson estimate: 62.37 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1502 / Rpim(I) all: 0.06936 / Rrim(I) all: 0.1657 / Net I/σ(I): 6.36
Reflection shellResolution: 2.65→2.77 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.457 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2530 / CC1/2: 0.687 / CC star: 0.903 / Rpim(I) all: 0.6839 / Rrim(I) all: 1.612 / % possible all: 95.71

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Processing

Software
NameVersionClassification
PHENIX2.0rc1_5599refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→48.28 Å / SU ML: 0.3059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1044
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 1070 9.96 %
Rwork0.2068 9673 -
obs0.2099 10743 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.47 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 85 83 1770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291723
X-RAY DIFFRACTIONf_angle_d0.53412331
X-RAY DIFFRACTIONf_chiral_restr0.0407245
X-RAY DIFFRACTIONf_plane_restr0.0043299
X-RAY DIFFRACTIONf_dihedral_angle_d17.4003670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.770.34481250.34831148X-RAY DIFFRACTION95.71
2.77-2.920.3851350.35611187X-RAY DIFFRACTION100
2.92-3.10.36691310.29931199X-RAY DIFFRACTION100
3.1-3.340.28091350.22971201X-RAY DIFFRACTION100
3.34-3.670.24191370.21891202X-RAY DIFFRACTION99.93
3.67-4.20.21031360.18361218X-RAY DIFFRACTION100
4.21-5.290.19221280.15341230X-RAY DIFFRACTION100
5.3-48.280.2041430.18451288X-RAY DIFFRACTION99.65

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