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- PDB-1js3: Crystal structure of dopa decarboxylase in complex with the inhib... -

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Basic information

Entry
Database: PDB / ID: 1js3
TitleCrystal structure of dopa decarboxylase in complex with the inhibitor carbidopa
ComponentsDOPA decarboxylaseAromatic L-amino acid decarboxylase
KeywordsLYASE / 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 / dopamine biosynthetic process / amino acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
dopa decarboxylase, N-terminal domain / dopa decarboxylase, N-terminal domain / Aromatic-L-amino-acid decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 ...dopa decarboxylase, N-terminal domain / dopa decarboxylase, N-terminal domain / Aromatic-L-amino-acid decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBIDOPA / PYRIDOXAL-5'-PHOSPHATE / Aromatic-L-amino-acid decarboxylase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsBurkhard, 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
DepositionAug 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DOPA decarboxylase
B: DOPA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,33510
Polymers108,0042
Non-polymers1,3318
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14480 Å2
ΔGint-146 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.360, 154.360, 86.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Cell settinghexagonal
Space group name H-MP62
DetailsThe asymmetric unit contains one dimer which is the biologically active oligomer

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Components

#1: Protein DOPA decarboxylase / Aromatic L-amino acid decarboxylase / E.C.4.1.1.28 / AROMATIC-L-AMINO-ACID DECARBOXYLASE / DDC


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 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-142 / CARBIDOPA / KINSON / 3-(3,4-DIHYDROXY-PHENYL)-2-HYDRAZINO-2-METHYL-PROPIONIC ACID / Carbidopa


Mass: 226.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
130 %(w/v)PEG5000 MME1reservoir
250 mMMES/KOH1reservoir
3400 mMammonium sulfate1reservoir
430.0 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 0.95 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMmodel building
CNS1refinement
DMphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2722 5.1 %RANDOM
Rwork0.144 ---
obs0.144 53582 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.5 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å22.14 Å20 Å2
2---0.34 Å20 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7250 0 82 455 7787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 418 5.3 %
Rwork0.18 7404 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3PARAM
X-RAY DIFFRACTION4PARAM
X-RAY DIFFRACTION5ION.PARAM
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor Rfree: 0.215 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.18

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