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- PDB-9hrh: Human holo aromatic L-amino acid decarboxylase (AADC) R347Q varia... -

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Basic information

Entry
Database: PDB / ID: 9hrh
TitleHuman holo aromatic L-amino acid decarboxylase (AADC) R347Q variant native structure
ComponentsAromatic-L-amino-acid decarboxylase
KeywordsLYASE / dopa decarboxylase / DDC / aromatic L-amino acid decarboxylase / AADC / R347Q variant
Function / homology
Function and homology information


aromatic-L-amino-acid decarboxylase / catecholamine biosynthetic process / carboxylic acid metabolic process / carboxy-lyase activity / amino acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Aromatic-L-amino-acid decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsPerduca, M. / Bisello, G. / Bertoldi, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateIIS154 United States
CitationJournal: Febs J. / Year: 2025
Title: The CRISPR-Cas9 knockout DDC SH-SY5Y in vitro model for AADC deficiency provides insight into the pathogenicity of R347Q and L353P variants: a cross-sectional structural and functional analysis.
Authors: Carmona-Carmona, C.A. / Bisello, G. / Franchini, R. / Lunardi, G. / Galavotti, R. / Perduca, M. / Ribeiro, R.P. / Belviso, B.D. / Giorgetti, A. / Caliandro, R. / Lievens, P.M. / Bertoldi, M.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,5513
Polymers54,1621
Non-polymers3882
Water6,359353
1
A: Aromatic-L-amino-acid decarboxylase
hetero molecules

A: Aromatic-L-amino-acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1016
Polymers108,3242
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area12480 Å2
ΔGint-58 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.270, 107.270, 218.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

21A-1022-

HOH

31A-1042-

HOH

41A-1050-

HOH

51A-1051-

HOH

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Components

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


Mass: 54162.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDC, hCG_1811384, tcag7.584 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53Y41, aromatic-L-amino-acid decarboxylase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Hepes, 40% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→72.95 Å / Num. obs: 82318 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 19.24 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 95933 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→53.64 Å / SU ML: 0.2093 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 4125 5.02 %
Rwork0.1996 78096 -
obs0.1999 82221 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→53.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 41 353 4032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293785
X-RAY DIFFRACTIONf_angle_d0.63145118
X-RAY DIFFRACTIONf_chiral_restr0.0428555
X-RAY DIFFRACTIONf_plane_restr0.0053654
X-RAY DIFFRACTIONf_dihedral_angle_d6.6686527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.41451620.38082628X-RAY DIFFRACTION100
1.72-1.740.35821320.35632653X-RAY DIFFRACTION99.96
1.74-1.760.34731340.32312654X-RAY DIFFRACTION100
1.76-1.790.29911410.28192641X-RAY DIFFRACTION99.93
1.79-1.810.28981220.28222662X-RAY DIFFRACTION99.89
1.81-1.840.28751410.2552642X-RAY DIFFRACTION99.89
1.84-1.860.23591260.24592642X-RAY DIFFRACTION99.89
1.86-1.890.23471460.2332661X-RAY DIFFRACTION100
1.89-1.920.22931430.23692650X-RAY DIFFRACTION100
1.92-1.960.20271200.2182689X-RAY DIFFRACTION100
1.96-1.990.22541520.22842636X-RAY DIFFRACTION100
1.99-2.030.22961520.23042660X-RAY DIFFRACTION100
2.03-2.070.2621380.23422667X-RAY DIFFRACTION100
2.07-2.120.22661560.20412636X-RAY DIFFRACTION99.89
2.12-2.170.19831350.20782666X-RAY DIFFRACTION99.82
2.17-2.220.18541490.19792673X-RAY DIFFRACTION100
2.22-2.280.22921540.18992674X-RAY DIFFRACTION100
2.28-2.350.23381330.19272684X-RAY DIFFRACTION100
2.35-2.420.22431570.18672658X-RAY DIFFRACTION100
2.42-2.510.20181550.18972694X-RAY DIFFRACTION100
2.51-2.610.20871280.1842704X-RAY DIFFRACTION100
2.61-2.730.19671420.18032701X-RAY DIFFRACTION99.96
2.73-2.870.19751340.18872700X-RAY DIFFRACTION100
2.87-3.050.17511360.18692743X-RAY DIFFRACTION99.9
3.05-3.290.19661480.18952714X-RAY DIFFRACTION99.97
3.29-3.620.19331560.1842742X-RAY DIFFRACTION100
3.62-4.140.14311430.17192784X-RAY DIFFRACTION99.97
4.15-5.220.18541390.16122820X-RAY DIFFRACTION99.97
5.22-53.640.18531510.19423018X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: 35.896035732 Å / Origin y: -33.6393345331 Å / Origin z: -9.21334617989 Å
111213212223313233
T0.126797542252 Å2-0.0096653948884 Å20.0103906510245 Å2-0.116389985895 Å20.0139457224749 Å2--0.121980987041 Å2
L0.499057212936 °2-0.0352282273058 °20.0345547078578 °2-0.446301685425 °2-0.0423318115924 °2--0.503234329172 °2
S-0.0225377131616 Å °-0.0253847967415 Å °-0.0757603757794 Å °0.0559043323974 Å °-0.00848244145252 Å °-0.0342570818846 Å °0.0703481792874 Å °-0.00771172531905 Å °0.0331059319451 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:714)

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