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- PDB-9nim: Structure of a K1305A mutant of the acyltransferase domain of Ncd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9nim | ||||||
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Title | Structure of a K1305A mutant of the acyltransferase domain of NcdE, a multi-domain NRPS protein from nocardichelin biosynthesis | ||||||
![]() | NcdE | ||||||
![]() | TRANSFERASE / acyltransferase / GNAT / siderophore biosynthesis / NRPS independent siderophores / NcdE-ATx | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fisk, M.B. / Gulick, A.M. / Barrera Ramirez, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.8 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.5 KB | Display | ![]() |
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Full document | ![]() | 421.5 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22440.115 Da / Num. of mol.: 1 / Fragment: acyltransferase domain / Mutation: K1305A Source method: isolated from a genetically manipulated source Details: N-terminal Gly His remain following cleavage of Histidine tag Source: (gene. exp.) ![]() ![]() ![]() References: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Chemical | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 8000 and 0.1M HEPES pH 7.5 adjusted by NaOH (7.16 mg/ml protein) |
-Data collection
Diffraction | Mean temperature: 113 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 4, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92019 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→69.82 Å / Num. obs: 31624 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.041 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.44→1.47 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.81 / Num. unique obs: 1588 / CC1/2: 0.59 / Rpim(I) all: 0.413 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→34.91 Å
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Refine LS restraints |
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LS refinement shell |
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