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Open data
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Basic information
Entry | Database: PDB / ID: 1js6 | ||||||
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Title | Crystal Structure of DOPA decarboxylase | ||||||
![]() | DOPA decarboxylase | ||||||
![]() | LYASE / DOPA decarboxylase / carbiDOPA / Parkinson's disease / Vitamin B6 | ||||||
Function / homology | ![]() L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / aromatic-L-amino-acid decarboxylase activity / serotonin biosynthetic process / catecholamine metabolic process / carboxylic acid metabolic process / amino acid metabolic process / dopamine biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Burkhard, P. / Dominici, P. / Borri-Voltattorni, C. / Jansonius, J.N. / Malashkevich, V.N. | ||||||
![]() | ![]() Title: Structural insight into Parkinson's disease treatment from drug-inhibited DOPA decarboxylase. Authors: Burkhard, P. / Dominici, P. / Borri-Voltattorni, C. / Jansonius, J.N. / Malashkevich, V.N. #1: ![]() Title: Preliminary X-ray analysis of a new crystal form of pig kidney DOPA decarboxylase Authors: Malashkevich, V.N. / Burkhard, P. / Dominici, P. / Moore, P.S. / Borri-Voltattorni, C. / Jansonius, J.N. #2: ![]() Title: Crystallization and preliminary X-ray analysis of pig kidney DOPA decarboxylase Authors: Malashkevich, V.N. / Filipponi, P. / Sauder, U. / Dominici, P. / Jansonius, J.N. / Borri-Voltattorni, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.2 KB | Display | ![]() |
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PDB format | ![]() | 155.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.2 KB | Display | ![]() |
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Full document | ![]() | 466.6 KB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 48.6 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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Unit cell |
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Components
#1: Protein | Mass: 54002.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P80041, aromatic-L-amino-acid decarboxylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.5 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5000, MES, ammonium sulfate at pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K | |||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.87 Å / Num. all: 31262 / Num. obs: 31262 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible obs: 67.8 % / Redundancy: 0.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.341 / % possible all: 67.8 |
Reflection | *PLUS Rmerge(I) obs: 0.086 |
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Processing
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Refinement | Resolution: 2.6→19.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2147993.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.18 Å2 / ksol: 0.333329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.352 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.291 |