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- PDB-9nom: Structure of the NIS synthetase NcdF from nocardichelin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 9nom
TitleStructure of the NIS synthetase NcdF from nocardichelin biosynthesis
ComponentsNcdF, a non-ribosomal independent siderophore synthetase
KeywordsLIGASE / NIS synthetase / siderophore biosynthesis / NRPS independent siderophores / NcdF
Function / homologyMALONATE ION
Function and homology information
Biological speciesNocardia carnea NBRC 14403 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 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
DepositionMar 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NcdF, a non-ribosomal independent siderophore synthetase
B: NcdF, a non-ribosomal independent siderophore synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,7074
Polymers137,5032
Non-polymers2042
Water00
1
A: NcdF, a non-ribosomal independent siderophore synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8542
Polymers68,7521
Non-polymers1021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NcdF, a non-ribosomal independent siderophore synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8542
Polymers68,7521
Non-polymers1021
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.544, 118.806, 168.202
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NcdF, a non-ribosomal independent siderophore synthetase


Mass: 68751.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal Gly His remain following cleavage of Histidine tag
Source: (gene. exp.) Nocardia carnea NBRC 14403 (bacteria) / Gene: ncdF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
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: 3.07 Å3/Da / Density % sol: 59.96 % / Description: Rod-shaped crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.6 M Sodium malonate and 0.1 M bis-tris propane pH 7 adjusted by HCl (16.35 mg/ml protein)

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Data collection

DiffractionMean temperature: 113 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: 2.87→50.7 Å / Num. obs: 39480 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 52.95 Å2 / CC1/2: 0.937 / Rmerge(I) obs: 0.325 / Rpim(I) all: 0.136 / Net I/σ(I): 4
Reflection shellResolution: 2.87→2.99 Å / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4402 / CC1/2: 0.654 / Rpim(I) all: 0.539

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→50.7 Å / SU ML: 0.4037 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2606 3784 5.07 %
Rwork0.2029 70852 -
obs0.2059 39394 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.22 Å2
Refinement stepCycle: LAST / Resolution: 2.87→50.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9003 0 14 0 9017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00839244
X-RAY DIFFRACTIONf_angle_d1.038512594
X-RAY DIFFRACTIONf_chiral_restr0.05461409
X-RAY DIFFRACTIONf_plane_restr0.00931641
X-RAY DIFFRACTIONf_dihedral_angle_d6.35241288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.910.39911260.32772664X-RAY DIFFRACTION99.61
2.91-2.940.38861630.31682591X-RAY DIFFRACTION99.71
2.94-2.980.31611320.30082634X-RAY DIFFRACTION99.78
2.98-3.030.39861430.2882628X-RAY DIFFRACTION99.64
3.03-3.070.31711420.27462597X-RAY DIFFRACTION99.75
3.07-3.120.35351280.26352661X-RAY DIFFRACTION99.82
3.12-3.170.2771330.25472630X-RAY DIFFRACTION99.78
3.17-3.230.33811300.25492663X-RAY DIFFRACTION99.86
3.23-3.290.29711440.24442574X-RAY DIFFRACTION99.96
3.29-3.350.26661440.24352603X-RAY DIFFRACTION99.96
3.35-3.420.30071400.23662669X-RAY DIFFRACTION99.93
3.42-3.490.2991360.22672649X-RAY DIFFRACTION99.86
3.49-3.570.27931350.20942597X-RAY DIFFRACTION99.71
3.57-3.660.24931330.20952646X-RAY DIFFRACTION98.97
3.66-3.760.25661350.19962618X-RAY DIFFRACTION99.96
3.76-3.870.27211550.18812610X-RAY DIFFRACTION99.96
3.87-40.23811110.18772667X-RAY DIFFRACTION99.93
4-4.140.23151460.17672604X-RAY DIFFRACTION99.96
4.14-4.30.20991570.18232623X-RAY DIFFRACTION99.93
4.3-4.50.23391310.16022627X-RAY DIFFRACTION99.93
4.5-4.740.25491630.1562625X-RAY DIFFRACTION99.75
4.74-5.030.22991410.16652635X-RAY DIFFRACTION100
5.03-5.420.28731310.18782625X-RAY DIFFRACTION98.71
5.42-5.970.28541520.19942578X-RAY DIFFRACTION100
5.97-6.830.26911490.19852627X-RAY DIFFRACTION100
6.83-8.590.1941590.1742634X-RAY DIFFRACTION99.96
8.6-50.70.17161250.16042573X-RAY DIFFRACTION97.97

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