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- PDB-6eem: Crystal structure of Papaver somniferum tyrosine decarboxylase in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6eem | ||||||
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Title | Crystal structure of Papaver somniferum tyrosine decarboxylase in complex with L-tyrosine | ||||||
![]() | (Tyrosine/dopa ...) x 2 | ||||||
![]() | LYASE / Aromatic Amino Acid Decarboxylase | ||||||
Function / homology | ![]() tyrosine decarboxylase / tyrosine decarboxylase activity / amino acid metabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Torrens-Spence, M.P. / Chiang, Y. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. Authors: Torrens-Spence, M.P. / Chiang, Y.C. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K. #1: ![]() Title: Structural basis for independent origins of new catalytic machineries in plant AAAD proteins Authors: Torrens-Spence, M.P. / Chiang, Y.-C. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 440.3 KB | Display | ![]() |
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PDB format | ![]() | 323.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6eeiC ![]() 6eeqC ![]() 6eewC ![]() 1js3S 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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Unit cell |
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Components on special symmetry positions |
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Components
-Tyrosine/dopa ... , 2 types, 2 molecules AB
#1: Protein | Mass: 56613.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O82415, aromatic-L-amino-acid decarboxylase |
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#2: Protein | Mass: 56841.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O82415, aromatic-L-amino-acid decarboxylase |
-Non-polymers , 4 types, 261 molecules ![](data/chem/img/0PR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TYR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-0PR / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-TYR / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.2 M ammonium Sulfate 0.1 Bis Tris pH 5.0 and 1% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→167 Å / Num. obs: 39550 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 34.2140174036 Å2 / CC1/2: 0.985 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.61→2.75 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5654 / CC1/2: 0.567 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JS3 Resolution: 2.61000662305→77.026298568 Å / SU ML: 0.337130549857 / Cross valid method: THROUGHOUT / σ(F): 1.32602802391 / Phase error: 23.3974781119
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.7978677589 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61000662305→77.026298568 Å
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Refine LS restraints |
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LS refinement shell |
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