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- PDB-3rbl: Crystal structure of Human aromatic L-amino acid decarboxylase (A... -

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Basic information

Entry
Database: PDB / ID: 3rbl
TitleCrystal structure of Human aromatic L-amino acid decarboxylase (AADC) in the apo form
Componentsaromatic L-amino acid decarboxylase
KeywordsLYASE / apo enzyme / apo form / open conformation / open dimer / exposed / conformational change / Parkinson / AADC deficiency / DDC / decarboxylase / PLP / L-DOPA
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 and melatonin biosynthesis / serotonin biosynthetic process / Catecholamine biosynthesis / catecholamine metabolic process / carboxylic acid metabolic process / amino acid metabolic process ...L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / aromatic-L-amino-acid decarboxylase activity / Serotonin and melatonin biosynthesis / serotonin biosynthetic process / Catecholamine biosynthesis / catecholamine metabolic process / carboxylic acid metabolic process / amino acid metabolic process / dopamine biosynthetic process / kidney development / response to toxic substance / pyridoxal phosphate binding / gene expression / enzyme binding / extracellular exosome / cytoplasm / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.24 Å
AuthorsGiardina, G. / Montioli, R. / Gianni, S. / Cellini, B. / Paiardini, A. / Borri Voltattorni, C. / Cutruzzola, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases.
Authors: Giardina, G. / Montioli, R. / Gianni, S. / Cellini, B. / Paiardini, A. / Voltattorni, C.B. / Cutruzzola, F.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)107,9623
Polymers107,9262
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-77 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.640, 179.640, 74.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

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


Mass: 53963.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AADC / Plasmid: pTrcHis2A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P20711, aromatic-L-amino-acid decarboxylase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion followed by soaking / pH: 7
Details: crystals obtained from holoAADC in 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0 were transferred in a ML droplet to yield apoAADC, vapor diffusion followed by soaking, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
51
61
71
81
91
101
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.24→127.025 Å / Num. all: 20098 / Num. obs: 20098 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.131 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueDiffraction-ID% possible all
3.24-3.416.20.4021.91782828860.4021100
3.41-3.626.50.2781.81773427180.2782100
3.62-3.876.50.1942.91677425750.1943100
3.87-4.186.50.1481.91577724290.1484100
4.18-4.586.50.1056.91422921980.105599.9
4.58-5.126.40.097.71299220290.09699.8
5.12-5.916.40.0947.71149918000.094799.8
5.91-7.246.30.1026.4962815320.102899.7
7.24-10.236.10.05211.8741412190.052999.5
10.23-49.8235.50.03814.839397120.0381097.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
EDNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rbf

3rbf


Resolution: 3.24→30 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.816 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.2019 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8284 / SU B: 28.076 / SU ML: 0.479 / SU R Cruickshank DPI: 0.5073 / SU Rfree: 0.5668 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.589 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2943 1019 5.1 %RANDOM
Rwork0.2361 ---
all0.239 20120 --
obs0.239 19980 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.86 Å2 / Biso mean: 46.6904 Å2 / Biso min: 25.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2--1.87 Å20 Å2
3----3.74 Å2
Refinement stepCycle: LAST / Resolution: 3.24→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6949 0 1 0 6950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227130
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9569645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85123.344317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.478151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8351550
X-RAY DIFFRACTIONr_chiral_restr0.0820.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215381
X-RAY DIFFRACTIONr_mcbond_it0.4641.54412
X-RAY DIFFRACTIONr_mcangle_it0.91927071
X-RAY DIFFRACTIONr_scbond_it1.35332718
X-RAY DIFFRACTIONr_scangle_it2.3964.52574
LS refinement shellResolution: 3.24→3.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 65 -
Rwork0.298 1368 -
all-1433 -
obs--100 %

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