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- PDB-9nil: Structure of a Y1216F mutant of the acyltransferase domain of Ncd... -

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Basic information

Entry
Database: PDB / ID: 9nil
TitleStructure of a Y1216F 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. / Barrera Ramirez, J.
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)22,7212
Polymers22,4821
Non-polymers2381
Water3,333185
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)33.489, 70.008, 37.099
Angle α, β, γ (deg.)90.000, 97.720, 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: 22482.217 Da / Num. of mol.: 1 / Fragment: acyltransferase domain / Mutation: Y1216F
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 8000 and 0.1M HEPES pH 7.5 adjusted with NaOH (10.23 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: Oct 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→70.01 Å / Num. obs: 30580 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Net I/σ(I): 20.8
Reflection shellResolution: 1.44→1.47 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1569 / CC1/2: 0.961 / Rpim(I) all: 0.103

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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→36.76 Å / SU ML: 0.1275 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.2905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1726 1545 5.06 %
Rwork0.1532 29010 -
obs0.1541 30555 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.59 Å2
Refinement stepCycle: LAST / Resolution: 1.44→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 15 185 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741544
X-RAY DIFFRACTIONf_angle_d0.97212094
X-RAY DIFFRACTIONf_chiral_restr0.0741221
X-RAY DIFFRACTIONf_plane_restr0.0103278
X-RAY DIFFRACTIONf_dihedral_angle_d5.7625228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.490.23721450.19282610X-RAY DIFFRACTION99.67
1.49-1.540.18381280.16632636X-RAY DIFFRACTION100
1.54-1.60.21871540.16372624X-RAY DIFFRACTION100
1.6-1.680.16581310.16092658X-RAY DIFFRACTION100
1.68-1.760.18451370.1622637X-RAY DIFFRACTION100
1.76-1.880.18781460.15482595X-RAY DIFFRACTION100
1.88-2.020.15771370.14552626X-RAY DIFFRACTION100
2.02-2.220.16961440.14232648X-RAY DIFFRACTION100
2.22-2.550.17491400.14772636X-RAY DIFFRACTION100
2.55-3.210.18011370.15292646X-RAY DIFFRACTION100
3.21-36.760.14821460.15032694X-RAY DIFFRACTION99.96

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