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- PDB-5n82: Crystal structure of an engineered TycA variant in complex with a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n82 | ||||||
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Title | Crystal structure of an engineered TycA variant in complex with an beta-Phe-AMP analog | ||||||
![]() | Tyrocidine synthase 1 | ||||||
![]() | LIGASE / nonribosomal peptide synthetase / adenylation domain | ||||||
Function / homology | ![]() phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / ligase activity / antibiotic biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niquille, D.L. / Hansen, D.L. / Mori, T. / Fercher, D. / Kries, H. / Hilvert, D. | ||||||
![]() | ![]() Title: Nonribosomal biosynthesis of backbone-modified peptides. Authors: Niquille, D.L. / Hansen, D.A. / Mori, T. / Fercher, D. / Kries, H. / Hilvert, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.7 KB | Display | ![]() |
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PDB format | ![]() | 75.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 816.8 KB | Display | ![]() |
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Full document | ![]() | 821 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n81C ![]() 1amuS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 47786.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P09095, phenylalanine racemase (ATP-hydrolysing) |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-BTB / |
#4: Chemical | ChemComp-8PZ / [( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris (pH 5.5) containing 200 mM (NH4)2SO4, 25% (v/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.708→50 Å / Num. obs: 48735 / % possible obs: 98.9 % / Redundancy: 6.78 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.25 |
Reflection shell | Resolution: 1.708→1.81 Å / Redundancy: 6.95 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.91 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1amu Resolution: 1.708→43.214 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.708→43.214 Å
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Refine LS restraints |
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LS refinement shell |
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