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- PDB-6ka3: Crystal structure of a Thebaine synthase from Papaver somniferum -

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Basic information

Entry
Database: PDB / ID: 6ka3
TitleCrystal structure of a Thebaine synthase from Papaver somniferum
ComponentsThebaine synthase 2
KeywordsBIOSYNTHETIC PROTEIN / synthase / crystallization
Function / homology
Function and homology information


thebaine synthase / carbon-oxygen lyase activity / alkaloid metabolic process / defense response / protein homodimerization activity
Similarity search - Function
: / Pathogenesis-related protein Bet v I family / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Thebaine synthase 2
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 Å
AuthorsXue, J. / Yu, X.J. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural insights into thebaine synthase 2 catalysis.
Authors: Chen, C.C. / Xue, J. / Peng, W. / Wang, B. / Zhang, L. / Liu, W. / Ko, T.P. / Huang, J.W. / Zhou, S. / Min, J. / Ma, L. / Dai, L. / Guo, R.T. / Yu, X.
History
DepositionJun 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thebaine synthase 2
B: Thebaine synthase 2
C: Thebaine synthase 2
D: Thebaine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0708
Polymers72,3654
Non-polymers7054
Water6,575365
1
A: Thebaine synthase 2
B: Thebaine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5354
Polymers36,1832
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-17 kcal/mol
Surface area14210 Å2
MethodPISA
2
C: Thebaine synthase 2
D: Thebaine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5354
Polymers36,1832
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-17 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.062, 43.882, 122.646
Angle α, β, γ (deg.)90.000, 127.300, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 13 or resid 15...
21(chain B and (resid 7 through 13 or resid 15...
31(chain C and (resid 7 through 13 or resid 15...
41(chain D and (resid 7 through 13 or resid 15...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain A and (resid 7 through 13 or resid 15...AA7 - 137 - 13
12THRTHRASPASP(chain A and (resid 7 through 13 or resid 15...AA15 - 2015 - 20
13ASPASPARGARG(chain A and (resid 7 through 13 or resid 15...AA22 - 7322 - 73
14VALVALASPASP(chain A and (resid 7 through 13 or resid 15...AA75 - 10475 - 104
15ILEILETHRTHR(chain A and (resid 7 through 13 or resid 15...AA106 - 121106 - 121
16ILEILELEULEU(chain A and (resid 7 through 13 or resid 15...AA124 - 154124 - 154
21SERSERLEULEU(chain B and (resid 7 through 13 or resid 15...BB7 - 137 - 13
22THRTHRASPASP(chain B and (resid 7 through 13 or resid 15...BB15 - 2015 - 20
23ASPASPARGARG(chain B and (resid 7 through 13 or resid 15...BB22 - 7322 - 73
24VALVALASPASP(chain B and (resid 7 through 13 or resid 15...BB75 - 10475 - 104
25ILEILETHRTHR(chain B and (resid 7 through 13 or resid 15...BB106 - 121106 - 121
26ILEILELEULEU(chain B and (resid 7 through 13 or resid 15...BB124 - 154124 - 154
31SERSERLEULEU(chain C and (resid 7 through 13 or resid 15...CC7 - 137 - 13
32THRTHRASPASP(chain C and (resid 7 through 13 or resid 15...CC15 - 2015 - 20
33ASPASPARGARG(chain C and (resid 7 through 13 or resid 15...CC22 - 7322 - 73
34VALVALASPASP(chain C and (resid 7 through 13 or resid 15...CC75 - 10475 - 104
35ILEILETHRTHR(chain C and (resid 7 through 13 or resid 15...CC106 - 121106 - 121
36ILEILELEULEU(chain C and (resid 7 through 13 or resid 15...CC124 - 154124 - 154
41SERSERLEULEU(chain D and (resid 7 through 13 or resid 15...DD7 - 137 - 13
42THRTHRASPASP(chain D and (resid 7 through 13 or resid 15...DD15 - 2015 - 20
43ASPASPARGARG(chain D and (resid 7 through 13 or resid 15...DD22 - 7322 - 73
44VALVALASPASP(chain D and (resid 7 through 13 or resid 15...DD75 - 10475 - 104
45ILEILETHRTHR(chain D and (resid 7 through 13 or resid 15...DD106 - 121106 - 121
46ILEILELEULEU(chain D and (resid 7 through 13 or resid 15...DD124 - 154124 - 154

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Components

#1: Protein
Thebaine synthase 2


Mass: 18091.283 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: THS2 / Plasmid: pET-46EK/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U9GGW3, thebaine synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.67 % / Mosaicity: 1.1 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M ammonium sulfate, 0.1M Bis-Tris, 8.0% v/v Acetone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2018
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25.058 Å / Num. obs: 46703 / % possible obs: 98.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 27.06 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.057 / Rrim(I) all: 0.137 / Χ2: 1.027 / Net I/σ(I): 11.9 / Num. measured all: 236529
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0230.31241510.9530.1720.3590.93188.1
2.02-2.13.60.30545290.9560.1650.3490.93895.8
2.1-2.24.20.29346570.9610.1520.3320.93299
2.2-2.314.80.28747200.9690.1410.3210.99999.9
2.31-2.465.40.25347150.9730.1180.280.999100
2.46-2.655.80.21747330.9750.0980.2391.001100
2.65-2.915.90.16847390.9840.0740.1841.096100
2.91-3.3360.13347740.9870.0580.1451.083100
3.33-4.25.90.10747730.9890.0470.1171.04299.8
4.2-255.80.09149120.9910.0410.11.09899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4REJ

4rej


Resolution: 1.951→25.058 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2355 2013 4.31 %
Rwork0.1903 --
obs0.1922 46655 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.82 Å2 / Biso mean: 39.7534 Å2 / Biso min: 12.92 Å2
Refinement stepCycle: final / Resolution: 1.951→25.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 46 365 5195
Biso mean--45.27 45.11 -
Num. residues----601
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2753X-RAY DIFFRACTION12.27TORSIONAL
12B2753X-RAY DIFFRACTION12.27TORSIONAL
13C2753X-RAY DIFFRACTION12.27TORSIONAL
14D2753X-RAY DIFFRACTION12.27TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9511-1.99990.32491210.24432642276381
1.9999-2.05390.26631440.22192942308692
2.0539-2.11430.26741360.21563128326497
2.1143-2.18250.24671470.2073218336599
2.1825-2.26050.29541460.206432203366100
2.2605-2.35090.28191450.204432553400100
2.3509-2.45790.30371440.193232463390100
2.4579-2.58730.2371510.196732363387100
2.5873-2.74920.27051410.192532633404100
2.7492-2.96120.24811400.199632683408100
2.9612-3.25860.24251490.194132453394100
3.2586-3.72880.20851450.168432823427100
3.7288-4.69290.19451510.165732833434100
4.6929-25.06040.21771530.196834143567100

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