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- PDB-6ebn: Crystal structure of Psilocybe cubensis noncanonical aromatic ami... -

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Basic information

Entry
Database: PDB / ID: 6ebn
TitleCrystal structure of Psilocybe cubensis noncanonical aromatic amino acid decarboxylase
Componentsnon canonical aromatic amino acid decarboxylase
KeywordsMETAL BINDING PROTEIN / Aromatic Amino Acid Decarboxylase
Function / homology
Function and homology information


carboxy-lyase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Fork head domain conserved site 2 / Fork head domain signature 2. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
FORMIC ACID / Non-canonical aromatic amino acid decarboxylase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96631108321 Å
AuthorsTorrens-Spence, M.P. / Chun-Ting, L. / Pluskal, T. / Chung, Y.K. / 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
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Monoamine Biosynthesis via a Noncanonical Calcium-Activatable Aromatic Amino Acid Decarboxylase in Psilocybin Mushroom.
Authors: Torrens-Spence, M.P. / Liu, C.T. / Pluskal, T. / Chung, Y.K. / Weng, J.K.
History
DepositionAug 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 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: non canonical aromatic amino acid decarboxylase
B: non canonical aromatic amino acid decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,12523
Polymers227,0202
Non-polymers1,10521
Water17,493971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20150 Å2
ΔGint-176 kcal/mol
Surface area69390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.723, 143.570, 71.408
Angle α, β, γ (deg.)90.000, 92.775, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein non canonical aromatic amino acid decarboxylase


Mass: 113510.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P1LYB6*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.5 M Sodium Formate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.96→123 Å / Num. obs: 169024 / % possible obs: 99.06 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.0859041966 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.58
Reflection shellResolution: 1.96→2 Å / Redundancy: 6.4 % / Num. unique obs: 7168 / CC1/2: 0.469 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSJ

5hsj


Resolution: 1.96631108321→71.785 Å / SU ML: 0.21615955403 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.8935550497
RfactorNum. reflection% reflection
Rfree0.197390589548 1813 1.18740421519 %
Rwork0.170497141824 --
obs0.170814691565 152686 89.7493019838 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.1104722326 Å2
Refinement stepCycle: LAST / Resolution: 1.96631108321→71.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15088 0 70 971 16129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010268772444315675
X-RAY DIFFRACTIONf_angle_d0.96837066850121314
X-RAY DIFFRACTIONf_chiral_restr0.06381479855422382
X-RAY DIFFRACTIONf_plane_restr0.00648382838682787
X-RAY DIFFRACTIONf_dihedral_angle_d18.86860419275752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9663-2.01950.327730966051140.311648496658960X-RAY DIFFRACTION69.4846466039
2.0195-2.07890.3362423284521060.27017548950410042X-RAY DIFFRACTION77.7386241765
2.0789-2.1460.2633166755221360.24342487183310437X-RAY DIFFRACTION81.0688544702
2.146-2.22270.2483412473641280.21929914397210993X-RAY DIFFRACTION85.1270667483
2.2227-2.31170.2534298601551310.203761011910979X-RAY DIFFRACTION85.1863211164
2.3117-2.41690.2377571682781410.18747128606911669X-RAY DIFFRACTION90.8112264514
2.4169-2.54440.2226132423641560.17896342271312031X-RAY DIFFRACTION92.9028815368
2.5444-2.70380.1980236936591350.17950990533612188X-RAY DIFFRACTION94.5232798957
2.7038-2.91250.1926689960841570.17782581836512422X-RAY DIFFRACTION96.0889160492
2.9125-3.20570.1925340799431520.17558622585912620X-RAY DIFFRACTION97.4887413175
3.2057-3.66950.1931778435891520.16166322683612744X-RAY DIFFRACTION98.3826670735
3.6695-4.62310.1392189998171470.13294257941712874X-RAY DIFFRACTION99.2000609477
4.6231-71.83280.1904964331841580.15218730344212914X-RAY DIFFRACTION98.4708097928

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