[English] 日本語
![](img/lk-miru.gif)
- PDB-7lkl: The internal aldimine form of the wild-type Salmonella typhimuriu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7lkl | ||||||
---|---|---|---|---|---|---|---|
Title | The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring | ||||||
![]() | (Tryptophan synthase ...) x 2 | ||||||
![]() | LYASE/LYASE INHIBITOR / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hilario, E. / Dunn, M.F. / Mueller, L.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the ...Title: The internal aldimine form of the wild-type Salmonella typhimurium Tryptophan Synthase in complex with inhibitor N-(4'-trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site and the product L-tryptophan at the enzyme beta-site at 1.05 Angstrom resolution. One of the beta-Q114 rotamer conformations allows a hydrogen bond to form with the PLP oxygen at the position 3 in the ring. Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 319.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 253.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 6.2 MB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cgqS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
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.) ![]() Gene: trpA, DD95_04145 / Plasmid: pBR322 / Details (production host): pEBA-10 / Production host: ![]() ![]() |
---|---|
#2: Protein | Mass: 42918.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trpB / Plasmid: pEBA-10 / Production host: ![]() ![]() |
-Non-polymers , 9 types, 878 molecules ![](data/chem/img/F9F.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/TRP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/TRP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-F9F / | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-DMS / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-CS / #8: Chemical | ChemComp-CL / #9: Chemical | #10: Chemical | ChemComp-PLP / | #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.88 % / Description: large plate-like crystal |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8 PH range: 7.6-8.0 / Temp details: constant |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: constant / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.88558 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→90.571 Å / Num. obs: 312765 / % possible obs: 93.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.076 / Rrim(I) all: 0.146 / Rsym value: 0.115 / Net I/av σ(I): 3.7 / Net I/σ(I): 4.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.595
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 312736 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5cgq Resolution: 1.05→28.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.239 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.06 Å2 / Biso mean: 12.923 Å2 / Biso min: 3.15 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.05→28.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|