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- PDB-6ka2: Crystal structure of a Thebaine synthase from Papaver somniferum ... -

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Basic information

Entry
Database: PDB / ID: 6ka2
TitleCrystal structure of a Thebaine synthase from Papaver somniferum in complex with TBN
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
Chem-D4R / Thebaine synthase 2
Similarity search - Component
Biological speciesPapaver somniferum (opium poppy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
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: Thebaine synthase 2
B: Thebaine synthase 2
C: Thebaine synthase 2
D: Thebaine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2997
Polymers72,3654
Non-polymers9343
Water3,891216
1
A: Thebaine synthase 2
B: Thebaine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8054
Polymers36,1832
Non-polymers6232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-7 kcal/mol
Surface area13830 Å2
MethodPISA
2
C: Thebaine synthase 2
D: Thebaine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4943
Polymers36,1832
Non-polymers3111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.080, 43.460, 118.803
Angle α, β, γ (deg.)90.000, 129.400, 90.000
Int Tables number5
Space group name H-MC121

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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-D4R / (4R,7aR,12bS)-7,9-dimethoxy-3-methyl-2,4,7a,13-tetrahydro-1H-4,12-methanobenzofuro[3,2-e]isoquinoline / Thebaine


Mass: 311.375 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H21NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.14 Å3/Da / Density % sol: 42.46 % / Mosaicity: 0.598 °
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: 2.29→25 Å / Num. obs: 27891 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.04 / Rrim(I) all: 0.082 / Χ2: 1.572 / Net I/σ(I): 12.6 / Num. measured all: 112428
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.29-2.374.10.627380.8420.3410.6921.289100
2.37-2.474.10.527450.8550.2840.5761.301100
2.47-2.584.10.39327820.8870.2230.4521.319100
2.58-2.714.10.27827590.9460.1580.321.417100
2.71-2.884.10.21727960.9650.1230.251.409100
2.88-3.114.10.1527750.9820.0850.1731.507100
3.11-3.424.10.07227660.9950.0410.0831.57100
3.42-3.9140.05328010.9970.030.0612.052100
3.91-4.923.90.03728230.9980.0210.0432.119100
4.92-253.80.0329060.9990.0170.0351.76999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4REJ

4rej


Resolution: 2.35→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.239 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.505 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1243 4.8 %RANDOM
Rwork0.1964 ---
obs0.1985 24699 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.75 Å2 / Biso mean: 51.749 Å2 / Biso min: 21.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å2-0 Å20.52 Å2
2---4.54 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 2.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 0 69 216 5054
Biso mean--73.75 52.61 -
Num. residues----598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134940
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184488
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6786684
X-RAY DIFFRACTIONr_angle_other_deg1.3061.61910501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62424.241257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16815896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6291520
X-RAY DIFFRACTIONr_chiral_restr0.070.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02942
LS refinement shellResolution: 2.35→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 78 -
Rwork0.304 1802 -
all-1880 -
obs--100 %

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