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- PDB-6eem: Crystal structure of Papaver somniferum tyrosine decarboxylase in... -

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Basic information

Entry
Database: PDB / ID: 6eem
TitleCrystal structure of Papaver somniferum tyrosine decarboxylase in complex with L-tyrosine
Components(Tyrosine/dopa ...) x 2
KeywordsLYASE / Aromatic Amino Acid Decarboxylase
Function / homology
Function and homology information


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
Chem-0PR / TYROSINE / Tyrosine decarboxylase
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61000662305 Å
AuthorsTorrens-Spence, M.P. / Chiang, Y. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins.
Authors: Torrens-Spence, M.P. / Chiang, Y.C. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K.
#1: Journal: Biorxiv / Year: 2019
Title: Structural basis for independent origins of new catalytic machineries in plant AAAD proteins
Authors: Torrens-Spence, M.P. / Chiang, Y.-C. / Smith, T. / Vicent, M.A. / Wang, Y. / Weng, J.K.
History
DepositionAug 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 20, 2020Group: Database references / Category: citation / citation_author
Revision 1.4Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine/dopa decarboxylase
B: Tyrosine/dopa decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,72211
Polymers113,4562
Non-polymers1,2669
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15470 Å2
ΔGint-202 kcal/mol
Surface area31550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.771, 122.771, 166.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-780-

HOH

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Components

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Tyrosine/dopa ... , 2 types, 2 molecules AB

#1: Protein Tyrosine/dopa decarboxylase


Mass: 56613.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: tydc9 / Production host: Escherichia coli (E. coli)
References: UniProt: O82415, aromatic-L-amino-acid decarboxylase
#2: Protein Tyrosine/dopa decarboxylase


Mass: 56841.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: tydc9 / Production host: Escherichia coli (E. coli)
References: UniProt: O82415, aromatic-L-amino-acid decarboxylase

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Non-polymers , 4 types, 261 molecules

#3: Chemical ChemComp-0PR / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine / PHOSPHO-5'-PYRIDOXYL TYROSINE


Type: L-peptide linking / Mass: 412.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N2O8P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2 M ammonium Sulfate 0.1 Bis Tris pH 5.0 and 1% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.61→167 Å / Num. obs: 39550 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 34.2140174036 Å2 / CC1/2: 0.985 / Net I/σ(I): 9.1
Reflection shellResolution: 2.61→2.75 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5654 / CC1/2: 0.567 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JS3

1js3


Resolution: 2.61000662305→77.026298568 Å / SU ML: 0.337130549857 / Cross valid method: THROUGHOUT / σ(F): 1.32602802391 / Phase error: 23.3974781119
RfactorNum. reflection% reflection
Rfree0.234528243478 1979 5.01456987204 %
Rwork0.18721148539 --
obs0.189602041113 39465 99.9594741775 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.7978677589 Å2
Refinement stepCycle: LAST / Resolution: 2.61000662305→77.026298568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 76 252 7952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004260051523547906
X-RAY DIFFRACTIONf_angle_d0.70894937717810740
X-RAY DIFFRACTIONf_chiral_restr0.04733285746771199
X-RAY DIFFRACTIONf_plane_restr0.004020893989351360
X-RAY DIFFRACTIONf_dihedral_angle_d17.51298473142838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.67530.34212122161280.2946076026372635X-RAY DIFFRACTION99.6753246753
2.6753-2.74760.3274294526811310.2716400523862620X-RAY DIFFRACTION99.9273519797
2.7476-2.82850.2928510645541490.2438717605842630X-RAY DIFFRACTION100
2.8285-2.91980.3116314497861440.2332167531472641X-RAY DIFFRACTION100
2.9198-3.02410.2841144279951530.2323041092972599X-RAY DIFFRACTION100
3.0241-3.14520.2950032533911230.2381497315672669X-RAY DIFFRACTION100
3.1452-3.28840.2495634084751430.2189759965882649X-RAY DIFFRACTION100
3.2884-3.46170.2823444923721230.1892640458852687X-RAY DIFFRACTION100
3.4617-3.67860.207148247111550.1666285720062634X-RAY DIFFRACTION100
3.6786-3.96260.1939421624381450.1549276435522690X-RAY DIFFRACTION100
3.9626-4.36140.19526442861540.1443731651032666X-RAY DIFFRACTION100
4.3614-4.99240.1870168020561600.1330825377312684X-RAY DIFFRACTION100
4.9924-6.28940.213619570541300.1699717572652773X-RAY DIFFRACTION100
6.2894-77.05980.1990799925251410.1774085483492909X-RAY DIFFRACTION99.8363338789

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