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- PDB-9nij: Structure of the acyltransferase domain of NcdE, a multi-domain N... -

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Basic information

Entry
Database: PDB / ID: 9nij
TitleStructure 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: 1.51 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)22,8293
Polymers22,4981
Non-polymers3302
Water3,009167
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)33.710, 69.980, 37.840
Angle α, β, γ (deg.)90.000, 97.530, 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: 22498.217 Da / Num. of mol.: 1 / Fragment: acyltransferase domain
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000 and 0.1 M of HEPES pH 7.5 adjusted with NaOH (14.7 mg/ml protein)

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.51→33.42 Å / Num. obs: 26508 / % possible obs: 96.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.75 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.054 / Net I/σ(I): 10.8
Reflection shellResolution: 1.51→1.59 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.7 / Num. unique obs: 3884 / CC1/2: 0.973 / Rpim(I) all: 0.071

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→33.42 Å / SU ML: 0.127 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 16.8007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1796 1340 5.06 %
Rwork0.1528 25162 -
obs0.1541 26502 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.03 Å2
Refinement stepCycle: LAST / Resolution: 1.51→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 21 167 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911516
X-RAY DIFFRACTIONf_angle_d1.0982050
X-RAY DIFFRACTIONf_chiral_restr0.0597212
X-RAY DIFFRACTIONf_plane_restr0.0131270
X-RAY DIFFRACTIONf_dihedral_angle_d11.2932222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.560.21981300.17352514X-RAY DIFFRACTION96.74
1.56-1.630.20231560.16442501X-RAY DIFFRACTION96.83
1.63-1.70.19091540.15332503X-RAY DIFFRACTION97.22
1.7-1.790.18251230.15512378X-RAY DIFFRACTION92.25
1.79-1.90.18181160.15072536X-RAY DIFFRACTION96.82
1.9-2.050.17331320.14062549X-RAY DIFFRACTION98.39
2.05-2.250.16461210.14252597X-RAY DIFFRACTION98.48
2.25-2.580.17521190.15142452X-RAY DIFFRACTION94.18
2.58-3.250.18141430.15272581X-RAY DIFFRACTION99.38
3.25-33.420.17551460.15682551X-RAY DIFFRACTION96.29

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