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Yorodumi- PDB-1js3: Crystal structure of dopa decarboxylase in complex with the inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1js3 | ||||||
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Title | Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa | ||||||
Components | DOPA decarboxylase | ||||||
Keywords | LYASE / DOPA decarboxylase / carbiDOPA / Parkinson's disease / Vitamin B6 | ||||||
Function / homology | Function and homology information 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 | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å | ||||||
Authors | Burkhard, P. / Dominici, P. / Borri-Voltattorni, C. / Jansonius, J.N. / Malashkevich, V.N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 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: Journal: Acta Crystallogr.,Sect.D / Year: 1999 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: Journal: J.Mol.Biol. / Year: 1992 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1js3.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1js3.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 1js3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1js3 ftp://data.pdbj.org/pub/pdb/validation_reports/js/1js3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit contains one dimer which is the biologically active oligomer |
-Components
#1: Protein | Mass: 54002.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: kidney / Plasmid: pKKDDC(delta)4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P80041, aromatic-L-amino-acid decarboxylase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.47 % | |||||||||||||||||||||||||
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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: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 0.95 Å |
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: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→19.61 Å / Num. all: 53582 / Num. obs: 53582 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.056 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.25→2.3 Å / % possible obs: 70.7 % / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.19 / % possible all: 70.7 |
Reflection | *PLUS Rmerge(I) obs: 0.056 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.25→19.61 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2350530.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.5 Å2 / ksol: 0.325 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.011 / 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: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.215 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.18 |