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- PDB-6liv: Crystal structure of Tyrosine decarboxylase in complex with PLP -

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Basic information

Entry
Database: PDB / ID: 6liv
TitleCrystal structure of Tyrosine decarboxylase in complex with PLP
ComponentsTyrosine/DOPA decarboxylase 2
KeywordsLYASE / holo 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: 2.31 Å
AuthorsWang, H. / Yu, J. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,73915
Polymers357,9106
Non-polymers8299
Water18,3391018
1
A: Tyrosine/DOPA decarboxylase 2
B: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6726
Polymers119,3032
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14420 Å2
ΔGint-92 kcal/mol
Surface area30990 Å2
MethodPISA
2
C: Tyrosine/DOPA decarboxylase 2
D: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7647
Polymers119,3032
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-93 kcal/mol
Surface area31000 Å2
MethodPISA
3
E: Tyrosine/DOPA decarboxylase 2
F: Tyrosine/DOPA decarboxylase 2


Theoretical massNumber of molelcules
Total (without water)119,3032
Polymers119,3032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-85 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.911, 180.414, 218.057
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: 59651.719 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1018 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: disodium malonate, HEPES, TCEP-HCl, glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / % possible obs: 99.7 % / Redundancy: 6.96 % / Biso Wilson estimate: 32.07 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.214 / Net I/σ(I): 7.12
Reflection shellResolution: 2.31→2.45 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 31999 / CC1/2: 0.712 / Rrim(I) all: 0.887 / % possible all: 98.4

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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: 2.31→49.84 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2499 10115 5 %
Rwork0.2265 192084 -
obs0.2277 202199 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.32 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22910 0 54 1018 23982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005223518
X-RAY DIFFRACTIONf_angle_d0.673331936
X-RAY DIFFRACTIONf_chiral_restr0.04733544
X-RAY DIFFRACTIONf_plane_restr0.00384049
X-RAY DIFFRACTIONf_dihedral_angle_d19.86518467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.340.34043110.29965871X-RAY DIFFRACTION92.21
2.34-2.370.31663340.27836337X-RAY DIFFRACTION99.97
2.37-2.390.29013360.27956401X-RAY DIFFRACTION100
2.39-2.420.29473340.2666313X-RAY DIFFRACTION99.97
2.42-2.460.30873360.26756422X-RAY DIFFRACTION100
2.46-2.490.31143310.25936346X-RAY DIFFRACTION99.96
2.49-2.530.30113380.26056348X-RAY DIFFRACTION100
2.53-2.560.28773390.26226396X-RAY DIFFRACTION99.99
2.56-2.60.28413280.25646363X-RAY DIFFRACTION100
2.6-2.650.26413390.24746373X-RAY DIFFRACTION99.99
2.65-2.690.30263380.25246423X-RAY DIFFRACTION99.99
2.69-2.740.28943360.25036332X-RAY DIFFRACTION99.96
2.74-2.790.27823370.24766407X-RAY DIFFRACTION99.97
2.79-2.850.27573320.24766360X-RAY DIFFRACTION100
2.85-2.910.27853400.24196400X-RAY DIFFRACTION99.97
2.91-2.980.26243370.246394X-RAY DIFFRACTION99.99
2.98-3.050.26683350.2336388X-RAY DIFFRACTION99.97
3.05-3.140.2523380.23416411X-RAY DIFFRACTION99.99
3.14-3.230.24643370.22466412X-RAY DIFFRACTION99.97
3.23-3.330.23123380.22096415X-RAY DIFFRACTION99.91
3.33-3.450.27053360.22126419X-RAY DIFFRACTION99.94
3.45-3.590.2563370.21496412X-RAY DIFFRACTION99.93
3.59-3.750.20553410.20166422X-RAY DIFFRACTION99.99
3.75-3.950.23363390.19746453X-RAY DIFFRACTION99.96
3.95-4.20.20743380.19576487X-RAY DIFFRACTION99.9
4.2-4.520.21973390.19696455X-RAY DIFFRACTION99.97
4.52-4.980.20143430.19826482X-RAY DIFFRACTION99.9
4.98-5.70.24513430.21926525X-RAY DIFFRACTION99.91
5.7-7.180.26173480.23696592X-RAY DIFFRACTION99.87
7.18-49.840.21553570.22016725X-RAY DIFFRACTION98.5

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