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- PDB-6am8: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6am8 | ||||||
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Title | Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9 with Trp bound as E(Aex2) | ||||||
![]() | (Tryptophan synthase beta chain ...) x 2 | ||||||
![]() | BIOSYNTHETIC PROTEIN / PLP Type II / Tryptophan Synthase / Engineered / Allostery | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Buller, A.R. / van Roye, P. | ||||||
![]() | ![]() Title: Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble. Authors: Buller, A.R. / van Roye, P. / Cahn, J.K.B. / Scheele, R.A. / Herger, M. / Arnold, F.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 602.1 KB | Display | ![]() |
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PDB format | ![]() | 494.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 57.1 KB | Display | |
Data in CIF | ![]() | 79.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vm5SC ![]() 6am7C ![]() 6am9C ![]() 6amcC ![]() 6amhC ![]() 6amiC 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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2 | ![]()
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Unit cell |
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Components
-Tryptophan synthase beta chain ... , 2 types, 4 molecules ADBC
#1: Protein | Mass: 43618.719 Da / Num. of mol.: 2 Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, V384A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: ![]() ![]() #2: Protein | Mass: 43390.602 Da / Num. of mol.: 2 Mutation: I16V, E17G, I68V, F95L, F274S, T292S, T321A, V384A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 416 molecules ![](data/chem/img/TRP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PLT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PLT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350 and 0.1 M Na HEPES pH 7.85 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→40 Å / Num. obs: 121628 / % possible obs: 99.2 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 24562 / CC1/2: 0.597 / Rpim(I) all: 0.864 / % possible all: 88.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VM5 Resolution: 1.83→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.655 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.626 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→40 Å
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Refine LS restraints |
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