+Open data
-Basic information
Entry | Database: PDB / ID: 1beu | ||||||
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Title | TRP SYNTHASE (D60N-IPP-SER) WITH K+ | ||||||
Components | (TRYPTOPHAN SYNTHASE) x 2 | ||||||
Keywords | CARBON-OXYGEN LYASE / MUTATION D60N IN A-SUBUNIT / INDOLE-3-PROPANOL PHOSPHATE IN A-SUBUNIT / L-SERINE IN B-SUBUNIT | ||||||
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 / ISOMORPHOUS WITH PDB ENTRY 1WSY / Resolution: 1.9 Å | ||||||
Authors | Rhee, S. / Mozzarelli, A. / Miles, E.W. / Davies, D.R. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Cryocrystallography and microspectrophotometry of a mutant (alpha D60N) tryptophan synthase alpha 2 beta 2 complex reveals allosteric roles of alpha Asp60. Authors: Rhee, S. / Miles, E.W. / Mozzarelli, A. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1beu.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1beu.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 1beu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1beu_validation.pdf.gz | 1013.9 KB | Display | wwPDB validaton report |
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Full document | 1beu_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1beu_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 1beu_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1beu ftp://data.pdbj.org/pub/pdb/validation_reports/be/1beu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 28697.812 Da / Num. of mol.: 1 / Mutation: CHAIN A, D60N Source method: isolated from a genetically manipulated source Details: LIGAND INDOLE-3-PROPANOL PHOSPHATE BOUND TO THE A-SUBUNIT AND L-SERINE BOUND TO THE B-SUBUNIT Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42973.039 Da / Num. of mol.: 1 / Mutation: CHAIN A, D60N Source method: isolated from a genetically manipulated source Details: LIGAND INDOLE-3-PROPANOL PHOSPHATE BOUND TO THE A-SUBUNIT AND L-SERINE BOUND TO THE B-SUBUNIT Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 330 molecules
#3: Chemical | ChemComp-IPL / |
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#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-PLS / [ |
#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: 2.4 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 50MM NABICINE (PH 7.8), 1MM NA-EDTA, 0.8-1.5MM SPERMINE, 12% PEG8000 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Ahmed, S.A., (1985) J. Biol. Chem., 260, 3716. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. obs: 49728 / % possible obs: 87 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 18.8 Å2 / Rsym value: 0.05 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 5 / Rsym value: 0.282 / % possible all: 63.3 |
Reflection | *PLUS Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 63.3 % / Rmerge(I) obs: 0.281 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: RFREE / σ(F): 2
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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