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- PDB-6am9: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6am9 | ||||||
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Title | Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser-bound in a predominantly closed state. | ||||||
![]() | Tryptophan synthase beta chain 1 | ||||||
![]() | LYASE / PLP Type II / Tryptophan Synthase / Engineered / Allostery / BIOSYNTHETIC PROTEIN | ||||||
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 | ![]() | 583.9 KB | Display | ![]() |
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PDB format | ![]() | 486.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 51.1 KB | Display | |
Data in CIF | ![]() | 70.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vm5SC ![]() 6am7C ![]() 6am8C ![]() 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
#1: Protein | Mass: 43390.602 Da / Num. of mol.: 4 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: Chemical | ChemComp-NA / #3: Chemical | ChemComp-PLS / [ | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.28 % |
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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: Aug 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→40 Å / Num. obs: 91166 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rpim(I) all: 0.03 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.09→2.13 Å / Redundancy: 6.9 % / Num. unique obs: 30761 / CC1/2: 0.695 / Rpim(I) all: 0.739 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5VM5 Resolution: 2.09→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 20.665 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.19 / 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: 60.15 Å2
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Refinement step | Cycle: 1 / Resolution: 2.09→40 Å
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Refine LS restraints |
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