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- PDB-9nnr: GNAT family acetyltransferase EryM in complex with Acetyl-CoA -

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Basic information

Entry
Database: PDB / ID: 9nnr
TitleGNAT family acetyltransferase EryM in complex with Acetyl-CoA
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 / ACETYL COENZYME *A / Lysine N-acyltransferase MbtK
Function and homology information
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: To Be Published
Title: Redefining the Role of the EryM Acetyltransferase in Natural Product Biosynthetic Pathways
Authors: Li, Y. / Smith, J. / Liu, X. / Harris, N. / Roberts, J. / Valdivia, E. / Ji, X.
History
DepositionMar 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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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)98,44520
Polymers95,4482
Non-polymers2,99718
Water70339
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.209, 153.209, 153.209
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-503-

MG

21B-505-

MG

31B-509-

SO4

41B-509-

SO4

51A-604-

HOH

61A-610-

HOH

71B-608-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 47723.871 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

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Non-polymers , 5 types, 57 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 277.14 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.8 M (NH4)2SO4, 3% (w/v) 2- methyl-2,4-pentanediol, 0.2 M NaCl, 0.1 M sodium cacodylate pH 5.8
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: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→48.45 Å / Num. obs: 26928 / % possible obs: 99.99 % / Redundancy: 20.4 % / Biso Wilson estimate: 58.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.216 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.03 Å / Rmerge(I) obs: 1.405 / Mean I/σ(I) obs: 2 / Num. unique obs: 2673 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.45 Å / SU ML: 0.3268 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.5667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 575 2.14 %
Rwork0.1869 26267 -
obs0.1877 26842 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.91 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6542 0 178 39 6759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046883
X-RAY DIFFRACTIONf_angle_d1.18569426
X-RAY DIFFRACTIONf_chiral_restr0.06071020
X-RAY DIFFRACTIONf_plane_restr0.01831242
X-RAY DIFFRACTIONf_dihedral_angle_d34.26412476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.28941400.25666524X-RAY DIFFRACTION100
3.19-3.650.29381450.19996485X-RAY DIFFRACTION99.98
3.66-4.60.2271410.1796540X-RAY DIFFRACTION100
4.6-48.450.181490.16486718X-RAY DIFFRACTION99.99

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