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- PDB-9hri: Human holo aromatic L-amino acid decarboxylase (AADC) L353P varia... -

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Basic information

Entry
Database: PDB / ID: 9hri
TitleHuman holo aromatic L-amino acid decarboxylase (AADC) L353P variant native structure
ComponentsAromatic-L-amino-acid decarboxylase
KeywordsLYASE / dopa decarboxylase / DDC / aromatic L-amino acid decarboxylase / AADC / L353P 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: 2.05 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
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,5643
Polymers54,1751
Non-polymers3882
Water4,216234
1
A: Aromatic-L-amino-acid decarboxylase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)109,1276
Polymers108,3512
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area11500 Å2
ΔGint-47 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.246, 107.246, 219.192
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-926-

HOH

21A-932-

HOH

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Components

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


Mass: 54175.270 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.: 234 / 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: 3.37 Å3/Da / Density % sol: 63.48 %
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: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→48.17 Å / Num. obs: 47570 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 30.66 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3632 / % 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: 2.05→48.17 Å / SU ML: 0.1753 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2093
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 2311 4.87 %
Rwork0.1889 45191 -
obs0.1899 47502 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 41 234 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283652
X-RAY DIFFRACTIONf_angle_d0.63094932
X-RAY DIFFRACTIONf_chiral_restr0.0419536
X-RAY DIFFRACTIONf_plane_restr0.0051630
X-RAY DIFFRACTIONf_dihedral_angle_d12.8027509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.2571280.21862594X-RAY DIFFRACTION100
2.09-2.140.24691360.20532615X-RAY DIFFRACTION99.96
2.14-2.190.19841260.20242624X-RAY DIFFRACTION100
2.19-2.240.24231550.19992576X-RAY DIFFRACTION100
2.24-2.30.23651290.19152616X-RAY DIFFRACTION100
2.3-2.370.22261470.19922593X-RAY DIFFRACTION100
2.37-2.450.22431460.19142624X-RAY DIFFRACTION100
2.45-2.530.22941340.19822611X-RAY DIFFRACTION100
2.53-2.640.20111230.18862639X-RAY DIFFRACTION100
2.64-2.760.2221240.18842652X-RAY DIFFRACTION100
2.76-2.90.20091470.18512645X-RAY DIFFRACTION100
2.9-3.080.18981390.18872631X-RAY DIFFRACTION100
3.08-3.320.21961330.20042676X-RAY DIFFRACTION99.96
3.32-3.650.20331320.18732688X-RAY DIFFRACTION99.96
3.65-4.180.21261400.17922697X-RAY DIFFRACTION100
4.18-5.270.18161420.16852758X-RAY DIFFRACTION100
5.27-48.170.21071300.19792952X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 35.541629788 Å / Origin y: -34.094728271 Å / Origin z: -9.18097718235 Å
111213212223313233
T0.199728789033 Å2-0.0224744027411 Å20.00866608486985 Å2-0.161072399127 Å20.0236183826881 Å2--0.185348173964 Å2
L0.55467244648 °2-0.043029077098 °20.0421247035258 °2-0.383426876336 °2-0.0625367584438 °2--0.614180331993 °2
S-0.0357870586795 Å °-0.0339699615166 Å °-0.0618260311484 Å °0.0532761147444 Å °-0.00331607039285 Å °-0.021123670623 Å °0.0863500603483 Å °-0.0284482151648 Å °0.0377970893231 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:714)

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