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- PDB-9oa7: GNAT family acetyltransferase EryM SeMet -

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Basic information

Entry
Database: PDB / ID: 9oa7
TitleGNAT family acetyltransferase EryM SeMet
ComponentsLysine N-acyltransferase MbtK
KeywordsTRANSFERASE / GNAT / acetyltransferase / erythrochelin
Function / homologyAcyltransferase MbtK/IucB-like, conserved domain / Siderophore biosynthesis protein domain / Acetyltransferase (GNAT) domain / N-acyltransferase activity / siderophore biosynthetic process / Acyl-CoA N-acyltransferase / Lysine N-acyltransferase MbtK
Function and homology information
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsLi, Y. / Smith, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM138396 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)DK042303 United States
CitationJournal: Structure / Year: 2025
Title: Redefining the role of the EryM acetyltransferase in natural product biosynthetic pathways.
Authors: Li, Y. / Liu, X. / Harris, N.R. / Roberts, J.R. / Valdivia, E.M. / Ji, X. / Smith, J.L.
History
DepositionApr 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 20, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine N-acyltransferase MbtK
B: Lysine N-acyltransferase MbtK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,19017
Polymers95,9172
Non-polymers1,27415
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-136 kcal/mol
Surface area40310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.940, 152.940, 152.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-511-

MG

21B-504-

MG

31A-622-

HOH

41A-655-

HOH

51B-626-

HOH

61B-638-

HOH

71B-650-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -18 through 144 or (resid 145...
d_2ens_1(chain "B" and (resid -18 through 129 or (resid 130...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11HISHISVALVALAA-18 - 3496 - 373
d_12ARGARGVALVALAA352 - 417376 - 441
d_13GOLGOLGOLGOLAC501
d_21HISHISVALVALBB-18 - 4176 - 441
d_22GOLGOLGOLGOLBN501

NCS oper: (Code: givenMatrix: (-0.648249348638, -0.28261973325, 0.707035266708), (-0.382102848837, -0.682436003214, -0.623119983974), (0.658612325197, -0.674097313372, 0.334398889358)Vector: 130. ...NCS oper: (Code: given
Matrix: (-0.648249348638, -0.28261973325, 0.707035266708), (-0.382102848837, -0.682436003214, -0.623119983974), (0.658612325197, -0.674097313372, 0.334398889358)
Vector: 130.480425576, 169.783234664, 15.1510066545)

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Components

#1: Protein Lysine N-acyltransferase MbtK / Mycobactin synthase protein K


Mass: 47958.340 Da / Num. of mol.: 2 / Mutation: L158F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: SACE_1304 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4F9A2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.8 M (NH4)2SO4, 3% (w/v) 2-methyl-2,4-pentanediol, 0.2 M NaCl, 0.1 M sodium cacodylate, pH 6
PH range: 5.8-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→48.36 Å / Num. obs: 1328601 / % possible obs: 99.99 % / Redundancy: 21 % / Biso Wilson estimate: 61.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Net I/σ(I): 19.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.473 / Num. unique obs: 7096 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→48.36 Å / SU ML: 0.3188 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6154
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 3533 4.97 %
Rwork0.1887 67502 -
obs0.1909 71035 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.99 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 73 109 6720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836773
X-RAY DIFFRACTIONf_angle_d1.04759264
X-RAY DIFFRACTIONf_chiral_restr0.05621013
X-RAY DIFFRACTIONf_plane_restr0.01431233
X-RAY DIFFRACTIONf_dihedral_angle_d34.73022429
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.47824090452 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.640.32381440.28642656X-RAY DIFFRACTION100
2.64-2.670.30741440.2632752X-RAY DIFFRACTION100
2.67-2.710.28761440.24242633X-RAY DIFFRACTION100
2.71-2.760.25491460.24092709X-RAY DIFFRACTION100
2.76-2.80.29681300.24412691X-RAY DIFFRACTION100
2.8-2.850.30441480.2242774X-RAY DIFFRACTION100
2.85-2.90.26581440.21142632X-RAY DIFFRACTION100
2.9-2.960.27561440.23962682X-RAY DIFFRACTION100
2.96-3.020.26451400.24282742X-RAY DIFFRACTION99.97
3.02-3.080.31191460.23742681X-RAY DIFFRACTION100
3.08-3.150.32731300.23912681X-RAY DIFFRACTION100
3.15-3.230.28881430.22672747X-RAY DIFFRACTION100
3.23-3.320.32381360.22052707X-RAY DIFFRACTION100
3.32-3.420.24071400.20192677X-RAY DIFFRACTION99.96
3.42-3.530.28661440.20082706X-RAY DIFFRACTION99.93
3.53-3.650.2371360.18992688X-RAY DIFFRACTION100
3.66-3.80.25181420.18422709X-RAY DIFFRACTION100
3.8-3.970.23271420.18052684X-RAY DIFFRACTION100
3.97-4.180.16321480.17272717X-RAY DIFFRACTION100
4.18-4.440.20491440.14942704X-RAY DIFFRACTION100
4.45-4.790.15231450.15592705X-RAY DIFFRACTION100
4.79-5.270.2191440.16922705X-RAY DIFFRACTION100
5.27-6.030.2621320.20192699X-RAY DIFFRACTION100
6.03-7.590.22791420.18892699X-RAY DIFFRACTION100
7.6-48.360.19661350.14572722X-RAY DIFFRACTION99.93

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