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Yorodumi- PDB-1a50: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a50 | ||||||
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Title | CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH 5-FLUOROINDOLE PROPANOL PHOSPHATE | ||||||
Components | (TRYPTOPHAN SYNTHASE ...) x 2 | ||||||
Keywords | LYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE | ||||||
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 / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 2.3 Å | ||||||
Authors | Schneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.-H. / Anderson, K.S. / Schlichting, I. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Loop closure and intersubunit communication in tryptophan synthase. Authors: Schneider, T.R. / Gerhardt, E. / Lee, M. / Liang, P.H. / Anderson, K.S. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a50.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a50.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a50_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 1a50_full_validation.pdf.gz | 468.7 KB | Display | |
Data in XML | 1a50_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1a50_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a50 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a50 | HTTPS FTP |
-Related structure data
Related structure data | 1a5sC 2wsyC 1wsy 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 natural source Details: INHIBITOR 5-FLUOROINDOLE PROPANOL PHOSPHATE BOUND TO THE ALPHA SITE Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42857.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: INHIBITOR 5-FLUOROINDOLE PROPANOL PHOSPHATE BOUND TO THE ALPHA SITE Source: (natural) Salmonella typhimurium (bacteria) / Cell line: CB149 / Plasmid: PSTB7 / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 241 molecules
#3: Chemical | ChemComp-FIP / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-PLP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: pH 7.8 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Nov 1, 1995 / Details: SYNCHROTRON |
Radiation | Monochromator: SYNCHROTRON / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→26.9 Å / Num. obs: 31823 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.29→2.34 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.4 / % possible all: 91.6 |
Reflection | *PLUS Highest resolution: 2.29 Å / Lowest resolution: 26.9 Å / Num. measured all: 66781 |
Reflection shell | *PLUS % possible obs: 91.6 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY. Starting model: 1WSY 1wsy Resolution: 2.3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.34 Å / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Num. reflection obs: 31627 / Rfactor obs: 0.164 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS |