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- PDB-8ora: Human holo aromatic L-amino acid decarboxylase (AADC) external al... -

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Basic information

Entry
Database: PDB / ID: 8ora
TitleHuman holo aromatic L-amino acid decarboxylase (AADC) external aldimine with L-Dopa methylester
ComponentsDopa decarboxylase (Aromatic L-amino acid decarboxylase)
KeywordsLYASE / Dopa decarboxilase / Human aromatic amino acid decarboxylase / AADC deficiency / L-dopa / dopamine / pyridoxal phosphate / PLP / Melevodopa / dopa methylester / DME / Catalytic loop
Function / homology
Function and homology information


aromatic-L-amino-acid decarboxylase / catecholamine biosynthetic process / carboxy-lyase activity / carboxylic acid metabolic process / 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
PYRIDOXAL-5'-PHOSPHATE / Chem-W5I / Aromatic-L-amino-acid decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsBisello, G. / Perduca, M. / Bertoldi, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other privateIIS PTCIT100263 Italy
CitationJournal: Protein Sci. / Year: 2023
Title: Human aromatic amino acid decarboxylase is an asymmetric and flexible enzyme: Implication in aromatic amino acid decarboxylase deficiency.
Authors: Bisello, G. / Ribeiro, R.P. / Perduca, M. / Belviso, B.D. / Polverino De' Laureto, P. / Giorgetti, A. / Caliandro, R. / Bertoldi, M.
History
DepositionApr 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,6164
Polymers53,9631
Non-polymers6533
Water2,000111
1
A: Dopa decarboxylase (Aromatic L-amino acid decarboxylase)
hetero molecules

A: Dopa decarboxylase (Aromatic L-amino acid decarboxylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2328
Polymers107,9262
Non-polymers1,3056
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area14990 Å2
ΔGint-77 kcal/mol
Surface area30690 Å2
Unit cell
Length a, b, c (Å)107.642, 107.642, 218.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

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Components

#1: Protein Dopa decarboxylase (Aromatic L-amino acid decarboxylase) / Dopa decarboxylase (Aromatic L-amino acid decarboxylase) / isoform CRA_a


Mass: 53963.195 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
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-W5I / methyl (2~{R})-2-azanyl-3-[3,4-bis(oxidanyl)phenyl]propanoate


Mass: 211.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.4→48.27 Å / Num. obs: 28904 / % possible obs: 97.2 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3001

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→29.89 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 1470 5.09 %
Rwork0.2127 --
obs0.2134 28886 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 43 111 3944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.505
X-RAY DIFFRACTIONf_dihedral_angle_d13.7491437
X-RAY DIFFRACTIONf_chiral_restr0.04575
X-RAY DIFFRACTIONf_plane_restr0.004679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.29021400.2572453X-RAY DIFFRACTION98
2.48-2.570.27081310.2462490X-RAY DIFFRACTION98
2.57-2.670.25891390.24712451X-RAY DIFFRACTION98
2.67-2.790.26171300.24972472X-RAY DIFFRACTION97
2.79-2.940.23371250.24282475X-RAY DIFFRACTION97
2.94-3.120.25411290.24642491X-RAY DIFFRACTION97
3.12-3.360.27091240.24422492X-RAY DIFFRACTION97
3.36-3.70.24781460.20872478X-RAY DIFFRACTION96
3.7-4.230.20491170.18932513X-RAY DIFFRACTION96
4.23-5.330.18191450.17272503X-RAY DIFFRACTION95
5.33-29.890.18891440.19422598X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 36.4955 Å / Origin y: -32.7828 Å / Origin z: -9.3399 Å
111213212223313233
T0.2752 Å2-0.0187 Å20.0089 Å2-0.2552 Å20.0289 Å2--0.2588 Å2
L0.5743 °2-0.0105 °2-0.0703 °2-0.5936 °2-0.1509 °2--0.8473 °2
S-0.0356 Å °-0.0171 Å °-0.0898 Å °0.0771 Å °0.0043 Å °-0.0586 Å °0.0765 Å °-0.0132 Å °0.0339 Å °
Refinement TLS groupSelection details: all

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