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- PDB-5ja2: EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ja2 | ||||||
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Title | EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the non-Native MbtH-Like Protein PA2412 | ||||||
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![]() | LIGASE / NONRIBOSOMAL PEPTIDE SYNTHETASE / NRPS / CONDENSATION / ADENYLATION / PCP / THIOESTERASE / MBTH-LIKE PROTEIN / PHOSPHOPANTETHEINE / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | ![]() L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / pyoverdine biosynthetic process / enterobactin synthetase complex / enterobactin biosynthetic process / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding ...L-serine-[L-seryl-carrier protein] ligase / enterobactin synthase / 2,3-dihydroxybenzoate-serine ligase activity / pyoverdine biosynthetic process / enterobactin synthetase complex / enterobactin biosynthetic process / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / nucleotidyltransferase activity / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, B.R. / Gulick, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture. Authors: Miller, B.R. / Drake, E.J. / Shi, C. / Aldrich, C.C. / Gulick, A.M. #1: ![]() Title: Structures of two distinct conformations of holo-non-ribosomal peptide synthetases. Authors: Drake, E.J. / Miller, B.R. / Shi, C. / Tarrasch, J.T. / Sundlov, J.A. / Allen, C.L. / Skiniotis, G. / Aldrich, C.C. / 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 | ![]() | 516.4 KB | Display | ![]() |
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PDB format | ![]() | 421.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.9 KB | Display | ![]() |
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Full document | ![]() | 746.3 KB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 60.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ja1SC 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: 142313.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: entF, b0586, JW0578 / Variant: W3110 / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: P11454, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||
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#2: Protein | Mass: 8649.739 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2412 / Plasmid: pET15b / Production host: ![]() ![]() | ||
#3: Chemical | ChemComp-75C / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Bis Tris propane, 50-150 mM MgCl2, and 15-28% Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 113.15 K / Ambient temp details: Liquid Nitrogen Gas Stream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3→58.98 Å / Num. obs: 31728 / % possible obs: 94.88 % / Redundancy: 3.1 % / Biso Wilson estimate: 65.6 Å2 / CC1/2: 0.914 / Rmerge(I) obs: 0.1026 / Net I/σ(I): 6.66 |
Reflection shell | Resolution: 3→3.107 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.6214 / Mean I/σ(I) obs: 1.37 / % possible all: 90.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JA1 Resolution: 3→58.974 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→58.974 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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