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Yorodumi- PDB-7mt4: Crystal structure of tryptophan Synthase in complex with F9, NH4+... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mt4 | ||||||
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Title | Crystal structure of tryptophan Synthase in complex with F9, NH4+, pH7.8 - alpha aminoacrylate form - E(A-A) | ||||||
Components | (Tryptophan synthase ...) x 2 | ||||||
Keywords | LYASE/INHIBITOR / PLP-dependent enzyme Tryptophan synthase / 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 enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Drago, V. / Hilario, E. / Dunn, M.F. / Mueser, T.C. / Mueller, L.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase alpha-aminoacrylate intermediate. Authors: Holmes, J.B. / Liu, V. / Caulkins, B.G. / Hilario, E. / Ghosh, R.K. / Drago, V.N. / Young, R.P. / Romero, J.A. / Gill, A.D. / Bogie, P.M. / Paulino, J. / Wang, X. / Riviere, G. / Bosken, Y.K. ...Authors: Holmes, J.B. / Liu, V. / Caulkins, B.G. / Hilario, E. / Ghosh, R.K. / Drago, V.N. / Young, R.P. / Romero, J.A. / Gill, A.D. / Bogie, P.M. / Paulino, J. / Wang, X. / Riviere, G. / Bosken, Y.K. / Struppe, J. / Hassan, A. / Guidoulianov, J. / Perrone, B. / Mentink-Vigier, F. / Chang, C.A. / Long, J.R. / Hooley, R.J. / Mueser, T.C. / 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 | 7mt4.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mt4.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 7mt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mt4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7mt4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7mt4_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 7mt4_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/7mt4 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/7mt4 | HTTPS FTP |
-Related structure data
Related structure data | 7mt5C 7mt6C 1tjpS S: Starting model for refinement 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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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 enterica subsp. enterica serovar Typhimurium (bacteria) Gene: trpA, DD95_04145 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6FWC1, tryptophan synthase |
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#2: Protein | Mass: 42918.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: trpB, STM1726 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 693 molecules
#3: Chemical | ChemComp-F9F / |
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#4: Chemical | ChemComp-0JO / |
#5: Chemical | ChemComp-NH4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 50 mM Bicine-NaOH pH 7.8, 10% PEG 8000, 2 mM spermine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.000014 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000014 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39.27 Å / Num. obs: 198056 / % possible obs: 98.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 13.37 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.4→1.48 Å / Num. unique obs: 6836 / CC1/2: 0.95 / Rpim(I) all: 0.146 / Rrim(I) all: 0.363 / Rsym value: 0.331 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1tjp Resolution: 1.4→36.31 Å / Cross valid method: FREE R-VALUE
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.95 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→36.31 Å
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Refine LS restraints |
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