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- PDB-8x0o: Crystal structure of Tyrosine decarboxylase H203F mutant in compl... -

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Basic information

Entry
Database: PDB / ID: 8x0o
TitleCrystal structure of Tyrosine decarboxylase H203F mutant in complex with the cofactor PLP and Tyrosine
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
TYROSINE / 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 H203F mutant in complex with the cofactor PLP and Tyrosine
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

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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)358,68910
Polymers357,9646
Non-polymers7254
Water00
1
A: Tyrosine/DOPA decarboxylase 2
B: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6844
Polymers119,3212
Non-polymers3622
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-92 kcal/mol
Surface area31130 Å2
MethodPISA
2
C: Tyrosine/DOPA decarboxylase 2
D: Tyrosine/DOPA decarboxylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6844
Polymers119,3212
Non-polymers3622
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13270 Å2
ΔGint-94 kcal/mol
Surface area31300 Å2
MethodPISA
3
E: Tyrosine/DOPA decarboxylase 2
F: Tyrosine/DOPA decarboxylase 2


Theoretical massNumber of molelcules
Total (without water)119,3212
Polymers119,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-86 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.550, 118.500, 181.880
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: 59660.742 Da / Num. of mol.: 6 / Mutation: H203F
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
#2: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.61 Å3/Da / Density % sol: 65.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sodium malonate 0.8M HEPES pH7.0 0.1M TCEP-HCl 0.005M Glycerol 4%

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→48.41 Å / Num. obs: 68655 / % possible obs: 99.74 % / Redundancy: 5.5 % / Biso Wilson estimate: 41.48 Å2 / CC1/2: 0.958 / Net I/σ(I): 4.99
Reflection shellResolution: 3.35→3.47 Å / Num. unique obs: 6698 / CC1/2: 0.703

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→48.41 Å / SU ML: 0.427 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2789 3427 5 %
Rwork0.2343 65167 -
obs0.2365 68594 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.82 Å2
Refinement stepCycle: LAST / Resolution: 3.35→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22888 0 50 0 22938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001323504
X-RAY DIFFRACTIONf_angle_d0.424631918
X-RAY DIFFRACTIONf_chiral_restr0.03753544
X-RAY DIFFRACTIONf_plane_restr0.00294048
X-RAY DIFFRACTIONf_dihedral_angle_d4.652813856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.40.36161420.30362630X-RAY DIFFRACTION97.67
3.4-3.450.34781400.28642660X-RAY DIFFRACTION99.75
3.45-3.50.31191410.27322717X-RAY DIFFRACTION100
3.5-3.560.33711390.26472674X-RAY DIFFRACTION100
3.56-3.620.35941420.25742677X-RAY DIFFRACTION99.93
3.62-3.680.32151440.24312667X-RAY DIFFRACTION99.86
3.68-3.760.27691400.23362707X-RAY DIFFRACTION99.96
3.76-3.830.2861380.23982711X-RAY DIFFRACTION100
3.83-3.920.26831410.24362654X-RAY DIFFRACTION99.75
3.92-4.010.26061460.23142716X-RAY DIFFRACTION99.97
4.01-4.110.2651450.21962696X-RAY DIFFRACTION99.96
4.11-4.220.25771410.20242698X-RAY DIFFRACTION99.89
4.22-4.340.24211440.21032703X-RAY DIFFRACTION99.96
4.34-4.480.24151370.21152677X-RAY DIFFRACTION100
4.48-4.640.25781380.20052729X-RAY DIFFRACTION100
4.64-4.830.23541500.21442712X-RAY DIFFRACTION99.76
4.83-5.050.27361390.21452724X-RAY DIFFRACTION99.97
5.05-5.310.25831460.23312720X-RAY DIFFRACTION99.9
5.31-5.640.31331440.24612742X-RAY DIFFRACTION99.93
5.64-6.080.28911420.25042734X-RAY DIFFRACTION99.72
6.08-6.690.29011470.25032747X-RAY DIFFRACTION99.93
6.69-7.650.26351420.23312758X-RAY DIFFRACTION99.86
7.65-9.630.22231480.21132807X-RAY DIFFRACTION99.9
9.63-48.410.29251510.23622907X-RAY DIFFRACTION98.87

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