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Yorodumi- PDB-6amc: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6amc | ||||||
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Title | Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11 | ||||||
Components | Tryptophan synthase beta chain 1 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / PLP Type II / Tryptophan Synthase / Engineered / Allostery | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Buller, A.R. / Herger, M. | ||||||
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 | 6amc.cif.gz | 589.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6amc.ent.gz | 488.4 KB | Display | PDB format |
PDBx/mmJSON format | 6amc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/6amc ftp://data.pdbj.org/pub/pdb/validation_reports/am/6amc | HTTPS FTP |
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-Related structure data
Related structure data | 5vm5C 6am7C 6am8C 6am9C 6amhC 6amiC 5dvzS C: citing same article (ref.) S: Starting model for refinement |
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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: 43694.816 Da / Num. of mol.: 4 / Mutation: T321A, T292S, F274S, I68V, E17G 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 | ChemComp-NA / #3: 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: 2.17 Å3/Da / Density % sol: 43.34 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40 Å / Num. obs: 114421 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rpim(I) all: 0.023 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5601 / CC1/2: 0.605 / Rpim(I) all: 0.547 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DVZ Resolution: 1.93→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.247 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.165 / 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: 50.408 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→40 Å
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Refine LS restraints |
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