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Yorodumi- PDB-6xsy: The external aldimine crystal structure of Salmonella typhimurium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xsy | ||||||
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Title | The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine (KOU) at the beta-site | ||||||
Components | (Tryptophan synthase ...) x 2 | ||||||
Keywords | LYASE/LYASE INHIBITOR / LYASE / Inhibitor complex / LYASE-LYASE INHIBITOR complex | ||||||
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 / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Hilario, E. / Mueller, L.J. / Dunn, M.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be Published Title: The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate ...Title: The external aldimine crystal structure of Salmonella typhimurium Tryptophan Synthase mutant beta-S377A with inhibitor 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate (F9F) at the alpha-site, Cesium ion at the metal coordination site, and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine (KOU) at the beta-site. Authors: Hilario, E. / Dunn, M.F. / Mueller, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xsy.cif.gz | 322.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xsy.ent.gz | 255.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xsy_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6xsy_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6xsy_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 6xsy_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/6xsy ftp://data.pdbj.org/pub/pdb/validation_reports/xs/6xsy | HTTPS FTP |
-Related structure data
Related structure data | 4hpxS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Tryptophan synthase ... , 2 types, 2 molecules AB
#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 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42902.879 Da / Num. of mol.: 1 / Mutation: S377A 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 / Plasmid: pEBA-10 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 7 types, 947 molecules
#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-F9F / | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-KOU / ( | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.51 Å3/Da / Density % sol: 50.94 % Description: plate-like crystal (0.20 mm x 0.15 mm x 0.30 mm) |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50 mM Bicine-CsOH, 7% PEG 8,000, 6 mM Spermine / PH range: 7.6-8.0 / Temp details: constant |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cobra System / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 15, 2020 / Details: Osmic Varimax HF ArcSec | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→90.44 Å / Num. all: 96776 / Num. obs: 96776 / % possible obs: 94.7 % / Redundancy: 4.1 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.057 / Rsym value: 0.033 / Net I/av σ(I): 13.8 / Net I/σ(I): 20.7 / Num. measured all: 399477 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 96759 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HPX Resolution: 1.55→38.91 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1921 / WRfactor Rwork: 0.149 / FOM work R set: 0.9103 / SU B: 2.362 / SU ML: 0.04 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.0752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 84.6 Å2 / Biso mean: 17.401 Å2 / Biso min: 5.3 Å2
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Refinement step | Cycle: final / Resolution: 1.55→38.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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