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

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Basic information

Entry
Database: PDB / ID: 3rbf
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 binding
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 biosynthetic process / catecholamine metabolic process / carboxylic 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 biosynthetic process / 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
PYRIDOXAL-5'-PHOSPHATE / Aromatic-L-amino-acid decarboxylase / Aromatic-L-amino-acid decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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

Downloads & links

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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)108,2445
Polymers107,9262
Non-polymers3183
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-85 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.840, 175.840, 74.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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, DDC, hCG_1811384, tcag7.584 / Plasmid: pTrcHis2A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q53Y41, UniProt: P20711*PLUS, aromatic-L-amino-acid decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 28-30% Jeffamine ED 2001 pH 7.0, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 22, 2010 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.9→28.77 Å / Num. all: 26640 / Num. obs: 26454 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 58.5 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 15.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3649 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1js6

1js6


Resolution: 2.9→28.77 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8221 / SU B: 39.648 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 1337 5.1 %RANDOM
Rwork0.2119 ---
all0.2147 26619 --
obs0.2147 26369 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.93 Å2 / Biso mean: 40.066 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--1.5 Å20 Å2
3----3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6954 0 18 0 6972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227130
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9569645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22223.344317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.732151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6441550
X-RAY DIFFRACTIONr_chiral_restr0.0890.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215381
X-RAY DIFFRACTIONr_mcbond_it0.4791.54412
X-RAY DIFFRACTIONr_mcangle_it0.97327071
X-RAY DIFFRACTIONr_scbond_it1.65332718
X-RAY DIFFRACTIONr_scangle_it2.8244.52574
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 90 -
Rwork0.272 1733 -
all-1823 -
obs--95.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2061-0.3916-0.9040.92791.95124.3017-0.03980.0314-0.07010.0661-0.0229-0.06810.149-0.20010.06270.11770.0302-0.00040.26570.01880.3032-66.0426-30.611-39.5051
26.07450.5821-0.09512.1211-0.48582.3225-0.01120.23720.1251-0.16880.12-0.1245-0.27090.0643-0.10880.13550.03450.03730.07770.00160.0215-47.4019-18.5974-12.5156
31.9746-2.25240.24.5439-0.30541.6524-0.00750.0303-0.3984-0.03270.08320.0590.18560.0553-0.07570.02730.03330.01370.21880.01830.1782-60.876-40.447-16.632
40.97090.01-1.29790.25330.59074.1504-0.008-0.0794-0.18320.00030.0945-0.0554-0.1091-0.1019-0.08650.11170.0616-0.03660.21470.06950.2058-64.5755-19.352-42.3255
56.2145-0.88272.45121.4443-0.54392.1606-0.0679-0.07640.03050.26880.0157-0.1671-0.09650.17680.05220.1960.0194-0.06750.0615-0.02440.0727-34.7433-18.4651-53.7379
61.12770.9455-0.5397.5891-0.76281.23990.30770.00690.20960.6789-0.22480.1507-0.6569-0.1938-0.08290.3590.08850.04630.11340.01810.046-57.0568-1.3878-57.9914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2A125 - 316
3X-RAY DIFFRACTION3A317 - 480
4X-RAY DIFFRACTION4B1 - 148
5X-RAY DIFFRACTION5B149 - 359
6X-RAY DIFFRACTION6B360 - 480

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