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

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Basic information

Entry
Database: PDB / ID: 8cvh
TitleStructure of L289F Hyoscyamine 6-beta Hydroxylase in complex with vanadyl, succinate, 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
FORMIC ACID / Chem-OVR / SUCCINIC ACID / STRONTIUM ION / VANADIUM ION / Hyoscyamine 6-beta-hydroxylase
Similarity search - Component
Biological speciesAtropa belladonna (belladonna)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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)43,90317
Polymers42,6671
Non-polymers1,23616
Water1,820101
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)44.915, 79.102, 56.276
Angle α, β, γ (deg.)90.000, 111.248, 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, 117 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#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-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
#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-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.: 101 / 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: 43.27 %
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: 2.03→50 Å / Num. obs: 23863 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.971 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.137 / Net I/σ(I): 6.63
Reflection shellResolution: 2.03→2.07 Å / Rmerge(I) obs: 1.715 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 1421 / CC1/2: 0.118 / Rpim(I) all: 1.102

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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: 2.03→43.752 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.29 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.189
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2495 1200 5.314 %
Rwork0.2011 21381 -
all0.203 --
obs-22581 95.002 %
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: 24.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.009 Å20 Å2
3----0.038 Å2
Refinement stepCycle: LAST / Resolution: 2.03→43.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 71 101 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172575
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.6543662
X-RAY DIFFRACTIONr_angle_other_deg1.1081.5775976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5535323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68224.882127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75815457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.797157
X-RAY DIFFRACTIONr_chiral_restr0.050.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
X-RAY DIFFRACTIONr_nbd_refined0.1880.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.22276
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21274
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2114
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.29
X-RAY DIFFRACTIONr_nbd_other0.1670.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0610.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.130.21
X-RAY DIFFRACTIONr_mcbond_it1.092.5081301
X-RAY DIFFRACTIONr_mcbond_other1.0892.5091302
X-RAY DIFFRACTIONr_mcangle_it1.8933.7491621
X-RAY DIFFRACTIONr_mcangle_other1.8933.7511622
X-RAY DIFFRACTIONr_scbond_it1.0862.7241408
X-RAY DIFFRACTIONr_scbond_other1.0852.7181403
X-RAY DIFFRACTIONr_scangle_it1.8923.9952041
X-RAY DIFFRACTIONr_scangle_other1.8913.9962042
X-RAY DIFFRACTIONr_lrange_it3.45329.1912873
X-RAY DIFFRACTIONr_lrange_other3.40929.1632860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.0830.355550.298924X-RAY DIFFRACTION56.2321
2.083-2.140.259690.2711340X-RAY DIFFRACTION82.1574
2.14-2.2020.308710.2631478X-RAY DIFFRACTION95.854
2.202-2.2690.314970.2671504X-RAY DIFFRACTION98.0404
2.269-2.3430.2981010.2491458X-RAY DIFFRACTION99.3627
2.343-2.4260.307850.2321400X-RAY DIFFRACTION99.7984
2.426-2.5170.319750.2251396X-RAY DIFFRACTION99.9321
2.517-2.6190.286930.2281317X-RAY DIFFRACTION100
2.619-2.7360.259910.2121248X-RAY DIFFRACTION100
2.736-2.8690.273610.2161221X-RAY DIFFRACTION100
2.869-3.0230.251600.2081177X-RAY DIFFRACTION100
3.023-3.2060.27710.2161101X-RAY DIFFRACTION100
3.206-3.4270.271570.1911019X-RAY DIFFRACTION100
3.427-3.70.216460.189969X-RAY DIFFRACTION100
3.7-4.0510.143530.162901X-RAY DIFFRACTION100
4.051-4.5260.165240.133832X-RAY DIFFRACTION100
4.526-5.2190.163330.143711X-RAY DIFFRACTION100
5.219-6.3770.196230.17623X-RAY DIFFRACTION100
6.377-8.9520.21210.157483X-RAY DIFFRACTION100
8.952-43.7520.251130.209277X-RAY DIFFRACTION98.9761

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