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- PDB-8yv7: X-ray structure of Thialysine N-epsilon-acetyltransferase from Ca... -

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Basic information

Entry
Database: PDB / ID: 8yv7
TitleX-ray structure of Thialysine N-epsilon-acetyltransferase from Caenorhabditis elegans
ComponentsThialysine N-epsilon-acetyltransferase
KeywordsTRANSFERASE / N-epsilon-acetyl-lysine / GNAT / Genetic code expansion
Function / homologyInterconversion of polyamines / : / N-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Acyl-CoA N-acyltransferase / Thialysine N-epsilon-acetyltransferase
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsWang, N. / Ma, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377058 China
CitationJournal: To Be Published
Title: Biosynthesis of N-epsilon-acetyl-lysine by GNAT
Authors: Wang, N. / Ma, X.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thialysine N-epsilon-acetyltransferase
B: Thialysine N-epsilon-acetyltransferase
C: Thialysine N-epsilon-acetyltransferase
D: Thialysine N-epsilon-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)74,6864
Polymers74,6864
Non-polymers00
Water00
1
A: Thialysine N-epsilon-acetyltransferase
B: Thialysine N-epsilon-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)37,3432
Polymers37,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-40 kcal/mol
Surface area15360 Å2
MethodPISA
2
C: Thialysine N-epsilon-acetyltransferase
D: Thialysine N-epsilon-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)37,3432
Polymers37,3432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-40 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.329, 65.098, 65.322
Angle α, β, γ (deg.)80.620, 72.760, 63.980
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Thialysine N-epsilon-acetyltransferase


Mass: 18671.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: D2023.4 / Production host: Escherichia coli (E. coli)
References: UniProt: O17731, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 16% w/v polyethylene glycol 8,000;20% v/v glycerol;40mM potasslum dl-hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9793 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.37→34.25 Å / Num. obs: 9322 / % possible obs: 81.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 64.04 Å2 / CC1/2: 0.919 / Net I/σ(I): 5.4
Reflection shellResolution: 3.37→3.49 Å / Num. unique obs: 9233 / CC1/2: 0.771

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.38→34.25 Å / SU ML: 0.4285 / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 31.4245
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2522 445 4.77 %
Rwork0.1828 8877 -
obs0.1865 9322 81.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.51 Å2
Refinement stepCycle: LAST / Resolution: 3.38→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 0 0 5261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01025389
X-RAY DIFFRACTIONf_angle_d1.37697278
X-RAY DIFFRACTIONf_chiral_restr0.0644776
X-RAY DIFFRACTIONf_plane_restr0.0107917
X-RAY DIFFRACTIONf_dihedral_angle_d7.9565697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.38-3.860.2865930.21791889X-RAY DIFFRACTION52.03
3.86-4.860.25421870.17533485X-RAY DIFFRACTION97.22
4.87-34.250.23961650.17773503X-RAY DIFFRACTION96.73

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