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- PDB-8egy: Engineered holo tyrosine synthase (TmTyrS1) derived from T. marit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8egy | ||||||
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Title | Engineered holo tyrosine synthase (TmTyrS1) derived from T. maritima TrpB | ||||||
![]() | Tryptophan synthase beta chain 1 | ||||||
![]() | BIOSYNTHETIC PROTEIN / tyrosine synthase / engineered enzyme / noncanonical amino acid synthase | ||||||
Function / homology | ![]() tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Porter, N.J. / Almhjell, P.J. / Arnold, F.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The beta-subunit of tryptophan synthase is a latent tyrosine synthase. Authors: Almhjell, P.J. / Johnston, K.E. / Porter, N.J. / Kennemur, J.L. / Bhethanabotla, V.C. / Ducharme, J. / Arnold, F.H. #1: Journal: J Appl Crystallogr / Year: 2007 Title: Phaser crystallographic software. Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: Features and development of Coot. Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan / ![]() Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.9 KB | Display | ![]() |
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PDB format | ![]() | 130.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8egzC ![]() 8eh0C ![]() 8eh1C ![]() 5dvzS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43701.777 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: engineered from tryptophan synthase beta chain 1 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 227 molecules ![](data/chem/img/PLP.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | The starting construct was tryptophan synthase beta chain 1, which was engineered to produce the ...The starting construct was tryptophan synthase beta chain 1, which was engineered to produce the construct used for expression and crystallization. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 1.2 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic, 0.1 M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), 0.1 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→39.15 Å / Num. obs: 69702 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 45.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.05→2.08 Å / Rmerge(I) obs: 2.017 / Num. unique obs: 4504 / CC1/2: 0.622 / Rpim(I) all: 0.58 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DVZ Resolution: 2.05→38.8 Å / SU ML: 0.3033 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9844 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→38.8 Å
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Refine LS restraints |
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LS refinement shell |
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