+Open data
-Basic information
Entry | Database: PDB / ID: 6iyk | |||||||||
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Title | The structure of EntE with 2-nitrobenzoyl adenylate analog | |||||||||
Components | 2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex | |||||||||
Keywords | LIGASE / adenylation / non-ribosomal peptide biosynthesis | |||||||||
Function / homology | Function and homology information (2,3-dihydroxybenzoyl)adenylate synthase / 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / enterobactin synthase / (2,3-dihydroxybenzoyl)adenylate synthase activity / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / siderophore biosynthetic process / acyltransferase activity / ligase activity / ATP binding ...(2,3-dihydroxybenzoyl)adenylate synthase / 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / enterobactin synthase / (2,3-dihydroxybenzoyl)adenylate synthase activity / 2,3-dihydroxybenzoate-serine ligase activity / enterobactin biosynthetic process / siderophore biosynthetic process / acyltransferase activity / ligase activity / ATP binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli 1303 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | |||||||||
Authors | Miyanaga, A. / Ishikawa, F. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket. Authors: Ishikawa, F. / Miyanaga, A. / Kitayama, H. / Nakamura, S. / Nakanishi, I. / Kudo, F. / Eguchi, T. / Tanabe, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iyk.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iyk.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 6iyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iyk ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iyk | HTTPS FTP |
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-Related structure data
Related structure data | 6iylC 3rg2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 0 / 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: 0 / 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.) Escherichia coli 1303 (bacteria) / Gene: entE, EC1303_c05680 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0E1LUI6, UniProt: P10378*PLUS, (2,3-dihydroxybenzoyl)adenylate synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2-methyl-2,4-pentanediol, HEPES-Na, 2-nitrobenzoyl-AMS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 25, 2018 |
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: 2.45→50 Å / Num. obs: 44501 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 30.106 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.06 / Rrim(I) all: 0.088 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4647 / CC1/2: 0.863 / Rpim(I) all: 0.355 / Rrim(I) all: 0.525 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RG2 Resolution: 2.45→45.34 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.491 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.268 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.975 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→45.34 Å
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Refine LS restraints |
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