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- PDB-7lt4: The aminoacrylate form of the beta-K167T mutant Tryptophan Syntha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lt4 | ||||||
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Title | The aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site | ||||||
![]() | (Tryptophan synthase ...) x 2 | ||||||
![]() | LYASE / inhibitor / aminoacrylate form / tryptophan synthase | ||||||
Function / homology | ![]() tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hilario, E. / Dunn, M.F. / Mueller, L.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the ...Title: The aminoacrylate form of the beta-K167T mutant Tryptophan Synthase at 1.80 Angstrom resolution in complex with N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site and cesium ion at the metal coordination site Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.8 KB | Display | ![]() |
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PDB format | ![]() | 231.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kwvS S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Tryptophan synthase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28698.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Plasmid: pEBA-10 / Production host: ![]() ![]() |
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#2: Protein | Mass: 42890.805 Da / Num. of mol.: 1 / Mutation: K167T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Plasmid: pEBA-10 / Production host: ![]() ![]() |
-Non-polymers , 8 types, 477 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/F9F.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/0JO.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/F9F.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/0JO.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-F9F / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-0JO / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % / Description: large plate-like crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 50 mM Bicine-CsOH, 8% PEG 8,000, 4 mM Spermine, pH 7.6 PH range: 7.60 -8.00 / Temp details: constant |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 6, 2020 / Details: VariMax HighFlux | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.796→91.394 Å / Num. obs: 65313 / % possible obs: 97 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.068 / Rrim(I) all: 0.123 / Rsym value: 0.087 / Net I/av σ(I): 5.3 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.433
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7KWV Resolution: 1.8→29.71 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.33 / 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: 95.76 Å2 / Biso mean: 26.9219 Å2 / Biso min: 3.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→29.71 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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Refinement TLS params. | Method: refined / Origin x: -24.084 Å / Origin y: -16.2389 Å / Origin z: 15.9466 Å
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Refinement TLS group |
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