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- PDB-1k3u: CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k3u | ||||||
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Title | CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID | ||||||
![]() | (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 | ![]() ![]() ![]() | ||||||
![]() | Weyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A. | ||||||
![]() | ![]() Title: Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase. Authors: Weyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157 KB | Display | ![]() |
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PDB format | ![]() | 119.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.7 KB | Display | ![]() |
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Full document | ![]() | 816.5 KB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k7eC ![]() 1k7fC ![]() 1qopS C: citing same article ( S: Starting model for refinement |
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Similar 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 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.) ![]() ![]() ![]() |
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#2: Protein | Mass: 42787.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 715 molecules ![](data/chem/img/IAD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IAD / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-PLP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2000 / Details: Premirror, Bent mirror |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31 Å / Num. obs: 77570 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.05 % / Rsym value: 0.048 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.7→1.8 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.123 / % possible all: 94.2 |
Reflection | *PLUS Lowest resolution: 31 Å / Num. measured all: 236589 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 94.2 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QOP Resolution: 1.7→20 Å / SU B: 1.91043 / SU ML: 0.06314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09026 / ESU R Free: 0.09174 / Stereochemistry target values: Engh & Huber Details: GLU 11 B exists in two conformations, each with 50% occupancy. With conformation A, HOH 709 exists. With conformation B, HOH 710 exists.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.909 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.8 Å / % reflection obs: 94.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1547 / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.153 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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