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- PDB-9nnq: GNAT family acetyltransferase EryM -

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Basic information

Entry
Database: PDB / ID: 9nnq
TitleGNAT family acetyltransferase EryM
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionMar 6, 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)96,74918
Polymers95,3802
Non-polymers1,37016
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-160 kcal/mol
Surface area40160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.846, 152.846, 152.846
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-501-

MG

21B-501-

MG

31A-626-

HOH

41B-647-

HOH

51B-674-

HOH

61B-736-

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 - 4176 - 441
d_12MGMGMGMGAC501
d_13SO4SO4SO4SO4AD502
d_14SO4SO4SO4SO4AE503
d_15SO4SO4SO4SO4AF504
d_21HISHISVALVALBB-18 - 4176 - 441
d_22MGMGMGMGBN501
d_23SO4SO4SO4SO4BO502
d_24SO4SO4SO4SO4BP503
d_25SO4SO4SO4SO4BQ504

NCS oper: (Code: givenMatrix: (-0.684693981442, -0.622307397329, -0.379377984345), (-0.671060945221, 0.335179425606, 0.661310789607), (-0.284378901425, 0.707381266277, -0.647101525685)Vector: 169. ...NCS oper: (Code: given
Matrix: (-0.684693981442, -0.622307397329, -0.379377984345), (-0.671060945221, 0.335179425606, 0.661310789607), (-0.284378901425, 0.707381266277, -0.647101525685)
Vector: 169.450134445, 14.8038771939, 130.245328743)

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Components

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


Mass: 47689.855 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.12 Å3/Da / Density % sol: 60.57 %
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-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→46.08 Å / Num. obs: 41204 / % possible obs: 99.79 % / Redundancy: 10.2 % / Biso Wilson estimate: 43.74 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1404 / Net I/σ(I): 8.63
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.063 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4044 / CC1/2: 0.503 / % possible all: 99.17

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.08 Å / SU ML: 0.2632 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.5646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2171 --
Rwork0.1786 39199 -
obs-41198 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 78 330 6957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00856787
X-RAY DIFFRACTIONf_angle_d1.04949285
X-RAY DIFFRACTIONf_chiral_restr0.0561015
X-RAY DIFFRACTIONf_plane_restr0.01211237
X-RAY DIFFRACTIONf_dihedral_angle_d13.66312438
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.53791155195 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.26721410.22412738X-RAY DIFFRACTION99.17
2.57-2.630.2691430.21212804X-RAY DIFFRACTION100
2.63-2.710.28471420.21972748X-RAY DIFFRACTION99.97
2.71-2.80.2711430.20922787X-RAY DIFFRACTION100
2.8-2.90.27051380.20912766X-RAY DIFFRACTION100
2.9-3.020.25921450.20592793X-RAY DIFFRACTION100
3.02-3.150.30451410.20052746X-RAY DIFFRACTION100
3.15-3.320.25811470.19122831X-RAY DIFFRACTION100
3.32-3.530.22741420.1862777X-RAY DIFFRACTION99.97
3.53-3.80.22791360.16412807X-RAY DIFFRACTION100
3.8-4.180.20751420.14792797X-RAY DIFFRACTION99.97
4.18-4.780.17121430.13592830X-RAY DIFFRACTION100
4.79-6.020.20371460.17072839X-RAY DIFFRACTION100
6.03-46.080.15271500.15712936X-RAY DIFFRACTION99.81

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