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- PDB-8b08: TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b08 | ||||||
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Title | TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plunger after 30 sec | ||||||
![]() | (Tryptophan synthase ...) x 2 | ||||||
![]() | LYASE / Trytophan Synthase / Time-resolved crystallography | ||||||
Function / homology | ![]() tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. ...Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography. Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / ...Authors: Mehrabi, P. / Sung, S. / von Stetten, D. / Prester, A. / Hatton, C.E. / Kleine-Dopke, S. / Berkes, A. / Gore, G. / Leimkohl, J.P. / Schikora, H. / Kollewe, M. / Rohde, H. / Wilmanns, M. / Tellkamp, F. / Schulz, E.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315 KB | Display | ![]() |
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PDB format | ![]() | 208.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aw8C ![]() 8aw9C ![]() 8awbC ![]() 8awcC ![]() 8awdC ![]() 8aweC ![]() 8awfC ![]() 8awsC ![]() 8awuC ![]() 8awvC ![]() 8awxC ![]() 8awyC ![]() 8b03C ![]() 8b05C ![]() 8b06C ![]() 8b2oC ![]() 8b2vC ![]() 8b2wC ![]() 8b3mC ![]() 2wsyS 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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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: 28836.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trpA, STM1727 / Production host: ![]() ![]() |
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#2: Protein | Mass: 42918.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: trpB, STM1726 / Production host: ![]() ![]() |
-Non-polymers , 5 types, 142 molecules ![](data/chem/img/G3P.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/PLS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CS.gif)
![](data/chem/img/PLS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-G3P / | ||
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#4: Chemical | ChemComp-CS / | ||
#5: Chemical | ChemComp-PLS / [ | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 300, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→45.46 Å / Num. obs: 25000 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.979 / Rmerge(I) obs: 0.398 / Rpim(I) all: 0.162 / Rrim(I) all: 0.43 / Net I/σ(I): 6.4 / Num. measured all: 172574 / Scaling rejects: 490 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WSY Resolution: 2.5→44.04 Å / SU ML: 0.276 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4284 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 39.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→44.04 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 65.8082905012 Å / Origin y: 17.8924987101 Å / Origin z: 15.5220967269 Å
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Refinement TLS group | Selection details: all |