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- PDB-2trs: CRYSTAL STRUCTURES OF MUTANT (BETAK87T) TRYPTOPHAN SYNTHASE ALPHA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2trs | ||||||
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Title | CRYSTAL STRUCTURES OF MUTANT (BETAK87T) TRYPTOPHAN SYNTHASE ALPHA2 BETA2 COMPLEX WITH LIGANDS BOUND TO THE ACTIVE SITES OF THE ALPHA AND BETA SUBUNITS REVEAL LIGAND-INDUCED CONFORMATIONAL CHANGES | ||||||
![]() | (TRYPTOPHAN SYNTHASE) x 2 | ||||||
![]() | LYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE | ||||||
Function / homology | ![]() tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Rhee, S. / Parris, K.D. / Hyde, C.C. / Ahmed, S.A. / Miles, E.W. / Davies, D.R. | ||||||
![]() | ![]() Title: Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes. Authors: Rhee, S. / Parris, K.D. / Hyde, C.C. / Ahmed, S.A. / Miles, E.W. / Davies, D.R. #1: ![]() Title: Lysine 87 in the Beta Subunit of Tryptophan Synthase that Forms an Internal Aldimine with Pyridoxal Phosphate Serves Critical Roles in Transimination, Catalysis, and Product Release Authors: Lu, Z. / Nagata, S. / Mcphie, P. / Miles, E.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.9 KB | Display | ![]() |
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PDB format | ![]() | 109.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986.9 KB | Display | ![]() |
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Full document | ![]() | 1005.5 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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: 28698.797 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T Source method: isolated from a genetically manipulated source Details: LIGAND INDOLE-3-PROPANOL PHOSPHATE BOUND TO THE ALPHA SUBUNIT AND L-SERINE BOUND TO THE BETA SUBUNIT Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 42944.965 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T Source method: isolated from a genetically manipulated source Details: LIGAND INDOLE-3-PROPANOL PHOSPHATE BOUND TO THE ALPHA SUBUNIT AND L-SERINE BOUND TO THE BETA SUBUNIT Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 192 molecules ![](data/chem/img/IPL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PLS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PLS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IPL / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-PLS / [ |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 grow | *PLUS Method: unknown / Details: pH is adjusted to 7.8 with NaOH | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 1993 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.04 Å / Num. obs: 37134 / % possible obs: 76.9 % / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.04→2.13 Å / Mean I/σ(I) obs: 2.1 / % possible all: 49 |
Reflection shell | *PLUS % possible obs: 49.4 % |
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Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY Resolution: 2.04→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
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Displacement parameters | Biso mean: 43.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.13 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.291 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.345 |