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- PDB-7c9m: The structure of product-bound CntL, an aminobutyrate transferase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c9m | ||||||
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Title | The structure of product-bound CntL, an aminobutyrate transferase in staphylopine biosynthesis | ||||||
![]() | D-histidine 2-aminobutanoyltransferase | ||||||
![]() | TRANSFERASE / Metallophore / Biosynthesis / product / Aminobutyrate | ||||||
Function / homology | D-histidine 2-aminobutanoyltransferase / nicotianamine synthase activity / nicotianamine biosynthetic process / Nicotianamine synthase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Chem-FN6 / 5'-DEOXY-5'-METHYLTHIOADENOSINE / D-histidine 2-aminobutanoyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, Z. / Zhou, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis. Authors: Luo, Z. / Luo, S. / Ju, Y. / Ding, P. / Xu, J. / Gu, Q. / Zhou, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413.3 KB | Display | ![]() |
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PDB format | ![]() | 342 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 37 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c7mSC ![]() 7c9kC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31858.998 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Mu50 / Gene: cntL, SAV2469 Production host: ![]() ![]() References: UniProt: A0A0H3JXA8, D-histidine 2-aminobutanoyltransferase #2: Chemical | ChemComp-FN6 / ( #3: Chemical | ChemComp-MTA / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3 M Magnesium formate dihydrate, 26% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 34032 / % possible obs: 96.8 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 3435 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C7M Resolution: 2.7→49.9 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.896 / SU B: 37.081 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R: 7.198 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.731 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→49.9 Å
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Refine LS restraints |
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