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- PDB-8cv9: Structure of Hyoscyamine 6-beta Hydroxylase in complex with vanad... -

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Basic information

Entry
Database: PDB / ID: 8cv9
TitleStructure of Hyoscyamine 6-beta Hydroxylase in complex with vanadyl, succinate, and hyoscyamine
ComponentsHyoscyamine 6-beta-hydroxylase
KeywordsOXIDOREDUCTASE / oxacyclase / scopolamine / epoxide
Function / homology
Function and homology information


hyoscyamine (6S)-dioxygenase / hyoscyamine (6S)-dioxygenase activity / coumarin biosynthetic process / response to molecule of fungal origin / L-ascorbic acid binding / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
FORMIC ACID / Chem-HYO / OXYGEN ATOM / SUCCINIC ACID / STRONTIUM ION / VANADIUM ION / Hyoscyamine 6-beta-hydroxylase
Similarity search - Component
Biological speciesAtropa belladonna (belladonna)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWenger, E.S. / Boal, A.K. / Bollinger, J.M. / Krebs, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113106 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Optimized Substrate Positioning Enables Switches in the C-H Cleavage Site and Reaction Outcome in the Hydroxylation-Epoxidation Sequence Catalyzed by Hyoscyamine 6 beta-Hydroxylase.
Authors: Wenger, E.S. / Martinie, R.J. / Ushimaru, R. / Pollock, C.J. / Sil, D. / Li, A. / Hoang, N. / Palowitch, G.M. / Graham, B.P. / Schaperdoth, I. / Burke, E.J. / Maggiolo, A.O. / Chang, W.C. / ...Authors: Wenger, E.S. / Martinie, R.J. / Ushimaru, R. / Pollock, C.J. / Sil, D. / Li, A. / Hoang, N. / Palowitch, G.M. / Graham, B.P. / Schaperdoth, I. / Burke, E.J. / Maggiolo, A.O. / Chang, W.C. / Allen, B.D. / Krebs, C. / Silakov, A. / Boal, A.K. / Bollinger Jr., J.M.
History
DepositionMay 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification
Revision 1.2May 21, 2025Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyoscyamine 6-beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,69915
Polymers42,6331
Non-polymers1,06614
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.970, 79.656, 56.017
Angle α, β, γ (deg.)90.000, 111.303, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hyoscyamine 6-beta-hydroxylase


Mass: 42632.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atropa belladonna (belladonna) / Gene: AbH6H, h6h / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XJ43, hyoscyamine (6S)-dioxygenase

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Non-polymers , 8 types, 309 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HYO / [(1S,5R)-8-methyl-8-azabicyclo[3.2.1]octan-3-yl] (2S)-3-hydroxy-2-phenylpropanoate


Mass: 289.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-V / VANADIUM ION


Mass: 50.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: V / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.45 % / Description: Bar
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium formate, strontium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 13, 2020
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 34661 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Net I/σ(I): 64.7
Reflection shellResolution: 1.79→1.81 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 28.1 / Num. unique obs: 1752 / CC1/2: 0.98 / Rpim(I) all: 0.048 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TTM

6ttm


Resolution: 1.79→28.086 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.961 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1921 1837 5.3 %
Rwork0.1738 32824 -
all0.175 --
obs-34661 99.747 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20 Å20.002 Å2
2---0.002 Å2-0 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.79→28.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 60 295 2942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132697
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172561
X-RAY DIFFRACTIONr_angle_refined_deg1.211.6633651
X-RAY DIFFRACTIONr_angle_other_deg1.1661.5895946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25224.961127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91315458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.079157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined0.1910.2483
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.22268
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21278
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2248
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.210
X-RAY DIFFRACTIONr_nbd_other0.1190.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1040.22
X-RAY DIFFRACTIONr_mcbond_it0.8171.5251301
X-RAY DIFFRACTIONr_mcbond_other0.8161.5261302
X-RAY DIFFRACTIONr_mcangle_it1.472.2751621
X-RAY DIFFRACTIONr_mcangle_other1.4692.2771622
X-RAY DIFFRACTIONr_scbond_it0.8391.6571396
X-RAY DIFFRACTIONr_scbond_other0.8361.6441389
X-RAY DIFFRACTIONr_scangle_it1.4232.4232030
X-RAY DIFFRACTIONr_scangle_other1.4232.4242031
X-RAY DIFFRACTIONr_lrange_it4.36919.1983015
X-RAY DIFFRACTIONr_lrange_other4.15918.6512937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.8360.2411360.2042360X-RAY DIFFRACTION97.5381
1.836-1.8860.1981380.1792362X-RAY DIFFRACTION99.96
1.886-1.9410.1931490.1792285X-RAY DIFFRACTION99.9589
1.941-2.0010.2211300.1882216X-RAY DIFFRACTION100
2.001-2.0660.2051240.1752176X-RAY DIFFRACTION100
2.066-2.1390.1931340.1712083X-RAY DIFFRACTION100
2.139-2.2190.1741080.1762006X-RAY DIFFRACTION100
2.219-2.310.1881010.1691949X-RAY DIFFRACTION100
2.31-2.4120.2011130.1771867X-RAY DIFFRACTION100
2.412-2.530.199940.1771772X-RAY DIFFRACTION100
2.53-2.6660.2151160.1741685X-RAY DIFFRACTION100
2.666-2.8270.181980.1641584X-RAY DIFFRACTION100
2.827-3.0220.223590.181540X-RAY DIFFRACTION100
3.022-3.2630.228510.1771455X-RAY DIFFRACTION100
3.263-3.5730.147670.1711286X-RAY DIFFRACTION100
3.573-3.9920.188760.1651175X-RAY DIFFRACTION99.8404
3.992-4.6060.161420.1491049X-RAY DIFFRACTION100
4.606-5.630.173470.17900X-RAY DIFFRACTION99.8945
5.63-7.9160.143380.177684X-RAY DIFFRACTION99.8617
7.916-28.0860.25160.203390X-RAY DIFFRACTION95.5294

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