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- PDB-8cvg: Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with... -

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Basic information

Entry
Database: PDB / ID: 8cvg
TitleStructure of L289F Hyoscyamine 6-beta Hydroxylase in complex with iron, 2-oxoglutarate, and 6-OH-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
2-OXOGLUTARIC ACID / : / FORMIC ACID / Chem-OVR / STRONTIUM ION / Hyoscyamine 6-beta-hydroxylase
Similarity search - Component
Biological speciesAtropa belladonna (belladonna)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,18222
Polymers42,6671
Non-polymers1,51521
Water4,720262
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)44.719, 79.228, 55.822
Angle α, β, γ (deg.)90.000, 111.027, 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: 42666.984 Da / Num. of mol.: 1 / Mutation: L289F
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 , 7 types, 283 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-OVR / (1R,3S,5R,6S)-6-hydroxy-8-methyl-8-azabicyclo[3.2.1]octan-3-yl (2S)-3-hydroxy-2-phenylpropanoate


Mass: 305.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SR / STRONTIUM ION


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


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 3, 2021
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 51478 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.906 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.04 / Net I/σ(I): 32.1
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 4 / Num. unique obs: 2573 / CC1/2: 0.906 / Rpim(I) all: 0.249 / % possible all: 100

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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: 1.56→43.572 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.29 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2006 2668 5.183 %
Rwork0.1817 48810 -
all0.183 --
obs-51478 99.603 %
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: 14.548 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å2-0 Å2-0.008 Å2
2--0.012 Å20 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.56→43.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 89 262 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132730
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172588
X-RAY DIFFRACTIONr_angle_refined_deg1.161.6563682
X-RAY DIFFRACTIONr_angle_other_deg1.191.5796005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33824.806129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49115458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.691157
X-RAY DIFFRACTIONr_chiral_restr0.0540.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02561
X-RAY DIFFRACTIONr_nbd_refined0.1950.2472
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.22304
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21149
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2220
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.211
X-RAY DIFFRACTIONr_nbd_other0.1150.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.080.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1180.21
X-RAY DIFFRACTIONr_mcbond_it0.751.4191305
X-RAY DIFFRACTIONr_mcbond_other0.7491.4221306
X-RAY DIFFRACTIONr_mcangle_it1.3622.121626
X-RAY DIFFRACTIONr_mcangle_other1.3622.1221627
X-RAY DIFFRACTIONr_scbond_it0.8071.5711425
X-RAY DIFFRACTIONr_scbond_other0.8071.5641422
X-RAY DIFFRACTIONr_scangle_it1.3512.2682056
X-RAY DIFFRACTIONr_scangle_other1.3512.272057
X-RAY DIFFRACTIONr_lrange_it3.41717.5383013
X-RAY DIFFRACTIONr_lrange_other3.28317.0852943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.2311870.2123435X-RAY DIFFRACTION94.8913
1.6-1.6440.2411870.2143512X-RAY DIFFRACTION99.8381
1.644-1.6920.2531730.2123430X-RAY DIFFRACTION99.9723
1.692-1.7440.211900.1973313X-RAY DIFFRACTION100
1.744-1.8010.2351810.1973225X-RAY DIFFRACTION100
1.801-1.8640.2231580.1923139X-RAY DIFFRACTION100
1.864-1.9340.2061530.1913004X-RAY DIFFRACTION100
1.934-2.0130.1861590.192897X-RAY DIFFRACTION100
2.013-2.1030.2051510.1842767X-RAY DIFFRACTION100
2.103-2.2050.1931620.1792651X-RAY DIFFRACTION100
2.205-2.3240.1921560.1712529X-RAY DIFFRACTION100
2.324-2.4650.2181160.1792387X-RAY DIFFRACTION100
2.465-2.6340.1851160.1782279X-RAY DIFFRACTION100
2.634-2.8450.2031140.1772091X-RAY DIFFRACTION100
2.845-3.1160.2361100.1871935X-RAY DIFFRACTION100
3.116-3.4820.1661040.1761746X-RAY DIFFRACTION100
3.482-4.0170.1751040.1641529X-RAY DIFFRACTION100
4.017-4.9130.182660.1511315X-RAY DIFFRACTION99.9276
4.913-6.9170.159470.1841040X-RAY DIFFRACTION100
6.917-43.5720.249340.181586X-RAY DIFFRACTION99.839

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