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- PDB-9nik: Structure of E1277A mutant of the acyltransferase domain of NcdE,... -

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Basic information

Entry
Database: PDB / ID: 9nik
TitleStructure of E1277A mutant of the acyltransferase domain of NcdE, a multi-domain NRPS protein from nocardichelin biosynthesis
ComponentsNcdE
KeywordsTRANSFERASE / acyltransferase / GNAT / siderophore biosynthesis / NRPS independent siderophores / NcdE-ATx
Biological speciesNocardia carnea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsFisk, M.B. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-136235 United States
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Identification and Characterization of the Biosynthesis of the Hybrid NRPS-NIS Siderophore Nocardichelin.
Authors: Fisk, M.B. / Barrera Ramirez, J. / Merrick, C.E. / Wencewicz, T.A. / Gulick, A.M.
History
DepositionFeb 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NcdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0476
Polymers22,4401
Non-polymers6075
Water3,063170
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)33.619, 69.650, 38.229
Angle α, β, γ (deg.)90.000, 96.320, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein NcdE


Mass: 22440.182 Da / Num. of mol.: 1 / Fragment: acyltransferase domain / Mutation: E1277A
Source method: isolated from a genetically manipulated source
Details: N-terminal Gly His remain following cleavage of Histidine tag
Source: (gene. exp.) Nocardia carnea (bacteria) / Strain: NBRC 14403 / Gene: ncdE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 8000 and 0.1 M of HEPES pH 7.5 adjusted with NaOH (16.33 mg/ml protein)

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92019 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.44→69.65 Å / Num. obs: 31587 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.026 / Net I/σ(I): 22.8
Reflection shellResolution: 1.44→1.47 Å / Rmerge(I) obs: 0.221 / Num. unique obs: 1559 / CC1/2: 0.96 / Rpim(I) all: 0.152

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→38 Å / SU ML: 0.1287 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.5571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1739 1583 5.02 %
Rwork0.1532 29978 -
obs0.1543 31561 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.81 Å2
Refinement stepCycle: LAST / Resolution: 1.44→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 39 170 1659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841574
X-RAY DIFFRACTIONf_angle_d1.01832135
X-RAY DIFFRACTIONf_chiral_restr0.0786228
X-RAY DIFFRACTIONf_plane_restr0.0192283
X-RAY DIFFRACTIONf_dihedral_angle_d6.5048243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.490.23241520.20432703X-RAY DIFFRACTION99.93
1.49-1.540.20061500.17032729X-RAY DIFFRACTION100
1.54-1.60.17291460.1592707X-RAY DIFFRACTION100
1.6-1.680.18081480.15772705X-RAY DIFFRACTION100
1.68-1.760.20471440.15922718X-RAY DIFFRACTION100
1.76-1.880.19171490.16172702X-RAY DIFFRACTION100
1.88-2.020.17391410.14142721X-RAY DIFFRACTION100
2.02-2.220.15691240.14262752X-RAY DIFFRACTION100
2.22-2.550.16471240.14372748X-RAY DIFFRACTION100
2.55-3.210.16381520.15342727X-RAY DIFFRACTION100
3.21-380.16691530.15192766X-RAY DIFFRACTION99.93

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