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- PDB-6liu: Crystal structure of apo Tyrosine decarboxylase -

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Basic information

Entry
Database: PDB / ID: 6liu
TitleCrystal structure of apo Tyrosine decarboxylase
ComponentsTyrosine/DOPA decarboxylase 2
KeywordsLYASE / apo form / decarboxylase / PLP binding / tyrosine
Function / homology
Function and homology information


L-dopa decarboxylase activity / 5-hydroxy-L-tryptophan decarboxylase activity / aromatic-L-amino-acid decarboxylase / tyrosine decarboxylase / tyrosine decarboxylase activity / 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
Tyrosine/DOPA decarboxylase 2
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYu, J. / Wang, H. / Yao, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H05424 Japan
Japan Society for the Promotion of Science (JSPS)19H04633 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structures clarify cofactor binding of plant tyrosine decarboxylase.
Authors: Wang, H. / Yu, J. / Satoh, Y. / Nakagawa, Y. / Tanaka, R. / Kato, K. / Yao, M.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)356,5426
Polymers356,5426
Non-polymers00
Water2,234124
1
A: Tyrosine/DOPA decarboxylase 2
B: Tyrosine/DOPA decarboxylase 2


Theoretical massNumber of molelcules
Total (without water)118,8472
Polymers118,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-87 kcal/mol
Surface area31190 Å2
MethodPISA
2
C: Tyrosine/DOPA decarboxylase 2
D: Tyrosine/DOPA decarboxylase 2


Theoretical massNumber of molelcules
Total (without water)118,8472
Polymers118,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-85 kcal/mol
Surface area30620 Å2
MethodPISA
3
E: Tyrosine/DOPA decarboxylase 2
F: Tyrosine/DOPA decarboxylase 2


Theoretical massNumber of molelcules
Total (without water)118,8472
Polymers118,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-79 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.043, 180.864, 217.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium malonate, HEPES, Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 114951 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 52.3 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.221 / Net I/σ(I): 7.37
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.07 / Num. unique obs: 18254 / CC1/2: 0.816 / Rrim(I) all: 0.98 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.16_3549refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JS3

1js3


Resolution: 2.8→48.13 Å / SU ML: 0.3411 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2796 5747 5.01 %
Rwork0.2415 109054 -
obs0.2434 114801 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21935 0 0 124 22059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005522475
X-RAY DIFFRACTIONf_angle_d0.716230513
X-RAY DIFFRACTIONf_chiral_restr0.13453410
X-RAY DIFFRACTIONf_plane_restr0.00463881
X-RAY DIFFRACTIONf_dihedral_angle_d21.2798093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.35911930.31493474X-RAY DIFFRACTION96.86
2.83-2.860.31111930.28993620X-RAY DIFFRACTION99.97
2.86-2.90.36031820.28733570X-RAY DIFFRACTION99.92
2.9-2.940.29791880.27123610X-RAY DIFFRACTION99.97
2.94-2.970.33671940.26973640X-RAY DIFFRACTION99.95
2.97-3.010.2871850.25763585X-RAY DIFFRACTION99.97
3.01-3.060.30171940.2593591X-RAY DIFFRACTION99.97
3.06-3.10.33261960.26843634X-RAY DIFFRACTION99.95
3.1-3.150.31461850.2733571X-RAY DIFFRACTION100
3.15-3.20.30041850.26433628X-RAY DIFFRACTION99.97
3.2-3.260.2951890.26543609X-RAY DIFFRACTION99.92
3.26-3.320.32031950.25423603X-RAY DIFFRACTION99.95
3.32-3.380.32471920.24593627X-RAY DIFFRACTION99.9
3.38-3.450.30391890.24433598X-RAY DIFFRACTION99.95
3.45-3.530.29121900.23723623X-RAY DIFFRACTION100
3.53-3.610.27981870.23583634X-RAY DIFFRACTION99.92
3.61-3.70.27221950.22823635X-RAY DIFFRACTION99.97
3.7-3.80.25571870.22483633X-RAY DIFFRACTION99.97
3.8-3.910.27061980.23263616X-RAY DIFFRACTION99.97
3.91-4.040.30261840.22963634X-RAY DIFFRACTION99.97
4.04-4.180.27081930.21873642X-RAY DIFFRACTION100
4.18-4.350.24211900.2233645X-RAY DIFFRACTION99.95
4.35-4.540.25221940.22283659X-RAY DIFFRACTION99.97
4.54-4.780.24861910.2143655X-RAY DIFFRACTION99.87
4.78-5.080.24771920.2263645X-RAY DIFFRACTION99.97
5.08-5.480.26431960.24283686X-RAY DIFFRACTION99.97
5.48-6.030.30471940.25493713X-RAY DIFFRACTION99.92
6.03-6.890.31151960.2623689X-RAY DIFFRACTION99.87
6.89-8.680.24371970.23173762X-RAY DIFFRACTION99.9
8.68-48.130.25332030.24263823X-RAY DIFFRACTION97.69

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