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- PDB-3k40: Crystal structure of Drosophila 3,4-dihydroxyphenylalanine decarb... -

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Basic information

Entry
Database: PDB / ID: 3k40
TitleCrystal structure of Drosophila 3,4-dihydroxyphenylalanine decarboxylase
ComponentsAromatic-L-amino-acid decarboxylase
KeywordsLYASE / PLP dependent protein / alpha beta protein / Alternative splicing / Catecholamine biosynthesis / Decarboxylase / Polymorphism / Pyridoxal phosphate / CG10697-PB isoform B
Function / homology
Function and homology information


anesthesia-resistant memory / adult chitin-containing cuticle pigmentation / Catecholamine biosynthesis / Serotonin and melatonin biosynthesis / regulation of adult chitin-containing cuticle pigmentation / serotonin biosynthetic process from tryptophan / aromatic-L-amino-acid decarboxylase / dopamine biosynthetic process from tyrosine / aromatic-L-amino-acid decarboxylase activity / wing disc development ...anesthesia-resistant memory / adult chitin-containing cuticle pigmentation / Catecholamine biosynthesis / Serotonin and melatonin biosynthesis / regulation of adult chitin-containing cuticle pigmentation / serotonin biosynthetic process from tryptophan / aromatic-L-amino-acid decarboxylase / dopamine biosynthetic process from tyrosine / aromatic-L-amino-acid decarboxylase activity / wing disc development / thermosensory behavior / serotonin biosynthetic process / catecholamine metabolic process / thermotaxis / carboxy-lyase activity / long-term memory / response to hydrogen peroxide / response to wounding / 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
Aromatic-L-amino-acid decarboxylase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP / Resolution: 1.75 Å
AuthorsHan, Q. / Ding, H. / Robinson, H. / Christensen, B.M. / Li, J.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure and substrate specificity of Drosophila 3,4-dihydroxyphenylalanine decarboxylase
Authors: Han, Q. / Ding, H. / Robinson, H. / Christensen, B.M. / Li, J.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aromatic-L-amino-acid decarboxylase
B: Aromatic-L-amino-acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8323
Polymers107,7392
Non-polymers921
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-82 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.809, 108.597, 86.294
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Aromatic-L-amino-acid decarboxylase / AADC / DOPA decarboxylase / DDC


Mass: 53869.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Description: Hypoderm isoform / Gene: CG10697, Ddc / Plasmid: PTYB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P05031, aromatic-L-amino-acid decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 4000, 20% glycerol, 200 mM CaCl2, and 100 mM Cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0908 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0908 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 100700 / Redundancy: 15.1 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.56

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLREP
Starting model: PDB entry 1js3

1js3


Resolution: 1.75→29.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4972 5 %RANDOM
Rwork0.19659 ---
obs0.19811 94557 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.005 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 6 601 7715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227293
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9549863
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5685892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58823.758330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.425151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8821544
X-RAY DIFFRACTIONr_chiral_restr0.1310.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.54456
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62127132
X-RAY DIFFRACTIONr_scbond_it2.44432837
X-RAY DIFFRACTIONr_scangle_it3.7624.52731
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 365 -
Rwork0.231 6811 -
obs--97.55 %

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