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- PDB-8x0p: Crystal structure of Tyrosine decarboxylase in complex with the c... -

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Basic information

Entry
Database: PDB / ID: 8x0p
TitleCrystal structure of Tyrosine decarboxylase in complex with the cofactor PLP and inhibitor carbidopa
ComponentsTyrosine/DOPA decarboxylase 2
KeywordsLYASE / complex / decarboxylase
Function / homology
Function and homology information


L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / tyrosine decarboxylase / tyrosine decarboxylase activity / aromatic-L-amino-acid decarboxylase / carboxylic acid metabolic process / amino acid metabolic process / pyridoxal phosphate binding / cytoplasm
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
CARBIDOPA / PYRIDOXAL-5'-PHOSPHATE / Tyrosine/DOPA decarboxylase 2
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsWang, H. / Yu, J. / Yao, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05424 Japan
Japan Society for the Promotion of Science (JSPS)19H04633 Japan
CitationJournal: To Be Published
Title: Crystal structure of Tyrosine decarboxylase in complex with the cofactor PLP and inhibitor carbidopa
Authors: Wang, H. / Yu, J. / Yao, M.
History
DepositionNov 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine/DOPA decarboxylase 2
B: Tyrosine/DOPA decarboxylase 2
C: Tyrosine/DOPA decarboxylase 2
D: Tyrosine/DOPA decarboxylase 2
E: Tyrosine/DOPA decarboxylase 2
F: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,38218
Polymers356,5426
Non-polymers2,84012
Water25214
1
A: Tyrosine/DOPA decarboxylase 2
B: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7946
Polymers118,8472
Non-polymers9474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14190 Å2
ΔGint-94 kcal/mol
Surface area31730 Å2
MethodPISA
2
C: Tyrosine/DOPA decarboxylase 2
D: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7946
Polymers118,8472
Non-polymers9474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-95 kcal/mol
Surface area31930 Å2
MethodPISA
3
E: Tyrosine/DOPA decarboxylase 2
F: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7946
Polymers118,8472
Non-polymers9474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-93 kcal/mol
Surface area32860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.540, 118.980, 182.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Tyrosine/DOPA decarboxylase 2


Mass: 59423.602 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: TYDC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P54769, aromatic-L-amino-acid decarboxylase, tyrosine decarboxylase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-142 / CARBIDOPA / KINSON / 3-(3,4-DIHYDROXY-PHENYL)-2-HYDRAZINO-2-METHYL-PROPIONIC ACID


Mass: 226.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sodium malonate 0.8M HEPES pH7.0 0.1M TECP-HCl 0.005M Glycerol 4%

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→49.84 Å / Num. obs: 69325 / % possible obs: 99.31 % / Redundancy: 6.9 % / Biso Wilson estimate: 57.61 Å2 / CC1/2: 0.981 / Net I/σ(I): 5.4
Reflection shellResolution: 3.35→3.47 Å / Num. unique obs: 6507 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→49.84 Å / SU ML: 0.4156 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.5824
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 3464 5 %
Rwork0.2141 65791 -
obs0.216 69255 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.03 Å2
Refinement stepCycle: LAST / Resolution: 3.35→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22785 0 186 14 22985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005123530
X-RAY DIFFRACTIONf_angle_d0.721231963
X-RAY DIFFRACTIONf_chiral_restr0.04693545
X-RAY DIFFRACTIONf_plane_restr0.00464053
X-RAY DIFFRACTIONf_dihedral_angle_d22.59318443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.390.37881250.29782259X-RAY DIFFRACTION86.56
3.39-3.440.32341360.26642622X-RAY DIFFRACTION99.86
3.44-3.490.36011350.25142612X-RAY DIFFRACTION99.93
3.49-3.550.27131330.24622590X-RAY DIFFRACTION99.82
3.55-3.60.29221430.23292648X-RAY DIFFRACTION99.89
3.6-3.670.28571430.23242584X-RAY DIFFRACTION99.82
3.67-3.730.25351310.21332631X-RAY DIFFRACTION99.96
3.73-3.80.2541430.21022622X-RAY DIFFRACTION99.86
3.8-3.880.2441330.21862613X-RAY DIFFRACTION100
3.88-3.970.22441370.20522671X-RAY DIFFRACTION99.93
3.97-4.060.2331390.20432570X-RAY DIFFRACTION99.93
4.06-4.160.22991350.2012629X-RAY DIFFRACTION100
4.16-4.270.22811420.19612638X-RAY DIFFRACTION100
4.27-4.40.23641400.20062633X-RAY DIFFRACTION100
4.4-4.540.26721370.19472624X-RAY DIFFRACTION99.89
4.54-4.70.19861410.18472644X-RAY DIFFRACTION100
4.7-4.890.20571370.18882629X-RAY DIFFRACTION99.89
4.89-5.110.25741400.19712652X-RAY DIFFRACTION99.96
5.11-5.380.22181400.20832663X-RAY DIFFRACTION100
5.38-5.720.25951390.22642666X-RAY DIFFRACTION99.96
5.72-6.160.25511390.22712643X-RAY DIFFRACTION99.78
6.16-6.780.27721410.2352689X-RAY DIFFRACTION99.86
6.78-7.760.26971410.2142698X-RAY DIFFRACTION99.93
7.76-9.760.19441460.19732733X-RAY DIFFRACTION100
9.76-49.840.27481480.21972828X-RAY DIFFRACTION99.03

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