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Yorodumi- PDB-5es9: Crystal structure of the LgrA initiation module in the formylatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5es9 | ||||||
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Title | Crystal structure of the LgrA initiation module in the formylation state | ||||||
Components | Linear gramicidin synthetase subunit A | ||||||
Keywords | LIGASE / NRPS / formylation domain / adenylation domain / peptidyl carrier protein / initiation module | ||||||
Function / homology | Function and homology information phosphopantetheine binding / ligase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Brevibacillus parabrevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 Å | ||||||
Authors | Reimer, J.M. / Aloise, M.N. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nature / Year: 2016 Title: Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. Authors: Reimer, J.M. / Aloise, M.N. / Harrison, P.M. / Schmeing, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5es9.cif.gz | 293.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5es9.ent.gz | 237.4 KB | Display | PDB format |
PDBx/mmJSON format | 5es9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/5es9 ftp://data.pdbj.org/pub/pdb/validation_reports/es/5es9 | HTTPS FTP |
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-Related structure data
Related structure data | 5es5C 5es6SC 5es7C 5es8C C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 88063.180 Da / Num. of mol.: 2 / Fragment: UNP residues 2-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70LM7 #2: Chemical | ChemComp-PNS / | |
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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: 4.51 Å3/Da / Density % sol: 72.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1 M AmSO4, 0.1 M bis-Tris pH 5.5, 3% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 200 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 21, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.77→48.45 Å / Num. obs: 32124 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 190.98 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.041 / Net I/av σ(I): 27.219 / Net I/σ(I): 7.3 / Num. measured all: 327215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ES6 Resolution: 3.77→48.45 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.12 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 541.5 Å2 / Biso mean: 261.0343 Å2 / Biso min: 160.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.77→48.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %
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