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- PDB-8k5t: The structure of EntE with2-methyl-3-chloro-benzoic acid sulfamoy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8k5t | ||||||
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Title | The structure of EntE with2-methyl-3-chloro-benzoic acid sulfamoyl adenosine | ||||||
![]() | Enterobactin synthase component E | ||||||
![]() | LIGASE / Adenylation / ATP binding / Nonribosomal peptide synthetase / Biosynthesis | ||||||
Function / homology | ![]() 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / acyltransferase activity / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miyanaga, A. / Ishikawa, F. | ||||||
Funding support | 1items
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![]() | ![]() Title: Reprogrammed aryl acid adenylation domain with an enlarged substrate binding pocket Authors: Ishikawa, F. / Miyanaga, A. / Kudo, F. / Eguchi, T. / Tanabe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.6 KB | Display | ![]() |
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PDB format | ![]() | 168.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 50.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k5sC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 3 - 528 / Label seq-ID: 3 - 528
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Components
#1: Protein | Mass: 61333.227 Da / Num. of mol.: 2 / Mutation: N235G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P10378, enterobactin synthase, 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase #2: Chemical | Mass: 498.897 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19ClN6O7S / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES-Na, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2022 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 29585 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4288 / CC1/2: 0.761 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 110.82 Å2 / Biso mean: 38.614 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 2.8→49.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16878 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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