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Yorodumi- PDB-5vm5: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vm5 | ||||||
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Title | Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9, with Ser bound | ||||||
Components | Tryptophan synthase beta chain 1 | ||||||
Keywords | LYASE / PLP / non-canonical amino acid / directed evolution / allostery | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å | ||||||
Authors | Buller, A.R. / van Roye, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vm5.cif.gz | 588.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vm5.ent.gz | 487.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/5vm5 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/5vm5 | HTTPS FTP |
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-Related structure data
Related structure data | 6am7C 6am8C 6am9C 6amcC 6amhC 6amiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8U093, tryptophan synthase #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-0JO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 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: 1.67→40 Å / Num. obs: 159409 / % possible obs: 99.7 % / Redundancy: 10 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.9 / CC1/2: 0.638 / Rpim(I) all: 0.894 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Resolution: 1.67→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.667 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.832 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→40 Å
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