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Yorodumi- PDB-5ja2: EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to ... -
+Open data
-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 | ||||||
Components |
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Keywords | LIGASE / NONRIBOSOMAL PEPTIDE SYNTHETASE / NRPS / CONDENSATION / ADENYLATION / PCP / THIOESTERASE / MBTH-LIKE PROTEIN / PHOSPHOPANTETHEINE / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Miller, B.R. / Gulick, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 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: Journal: Nature / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ja2.cif.gz | 516.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ja2.ent.gz | 421.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ja2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ja2_validation.pdf.gz | 735.9 KB | Display | wwPDB validaton report |
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Full document | 5ja2_full_validation.pdf.gz | 746.3 KB | Display | |
Data in XML | 5ja2_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 5ja2_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/5ja2 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/5ja2 | HTTPS FTP |
-Related structure data
Related structure data | 5ja1SC 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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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.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: entF, b0586, JW0578 / Variant: W3110 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2412 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I169 | ||
#3: Chemical | ChemComp-75C / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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