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Yorodumi- PDB-8eys: X-ray crystal structure of salmonella typhimurium Tryptophan synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eys | ||||||
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Title | X-ray crystal structure of salmonella typhimurium Tryptophan synthase internal aldimine at pH 5.0 | ||||||
Components |
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Keywords | LYASE / beta-elimination / PLP-dependent | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Drago, V.N. / Kovalevsky, A.Y. / Mueser, T.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep Phys Sci / Year: 2024 Title: Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. Authors: Drago, V.N. / Devos, J.M. / Blakeley, M.P. / Forsyth, V.T. / Parks, J.M. / Kovalevsky, A. / Mueser, T.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eys.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eys.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 8eys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eys_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 8eys_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 8eys_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 8eys_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/8eys ftp://data.pdbj.org/pub/pdb/validation_reports/ey/8eys | HTTPS FTP |
-Related structure data
Related structure data | 8eypC 8ezcC 1bksS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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
#1: Protein | Mass: 28698.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpA, STM1727 / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 43146.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: trpB, STM1726 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 50 mM Bicine pH 7.8, 1 mM EDTA, 0.2 mM PLP, 2 mM spermine, and 6% PEG 8000; acidified with sodium acetate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.58 Å / Num. obs: 37370 / % possible obs: 96.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Num. unique obs: 5337 / CC1/2: 0.906 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bks Resolution: 2.2→16.54 Å / Cross valid method: THROUGHOUT / σ(F): 0.11 / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.81 Å2 / Biso mean: 37.94 Å2 / Biso min: 13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→16.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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