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

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Basic information

Entry
Database: PDB / ID: 8cvf
TitleStructure of L289F 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: 1.532 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)43,67114
Polymers42,6671
Non-polymers1,00413
Water6,557364
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)44.783, 79.901, 55.675
Angle α, β, γ (deg.)90.000, 111.244, 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 , 8 types, 377 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: 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 / Comment: alkaloid, toxin*YM
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / 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-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.: 364 / 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: 2.16 Å3/Da / Density % sol: 43.07 % / 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: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 52983 / % possible obs: 97 % / Redundancy: 5.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.053 / Net I/σ(I): 26.4
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2524 / CC1/2: 0.839 / Rpim(I) all: 0.278 / % possible all: 92.6

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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: 1.532→43.557 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.238 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2011 2526 4.768 %
Rwork0.1809 50457 -
all0.182 --
obs-52983 96.549 %
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: 14.504 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0 Å2-0.007 Å2
2--0.01 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.532→43.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 56 364 2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172540
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.6623630
X-RAY DIFFRACTIONr_angle_other_deg1.2761.5895897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7245321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24924.841126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8215453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.464157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
X-RAY DIFFRACTIONr_nbd_refined0.2050.2481
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.22275
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21297
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3550.212
X-RAY DIFFRACTIONr_nbd_other0.2420.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.213
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0430.23
X-RAY DIFFRACTIONr_mcbond_it0.7251.3861293
X-RAY DIFFRACTIONr_mcbond_other0.7251.3871294
X-RAY DIFFRACTIONr_mcangle_it1.2842.0721611
X-RAY DIFFRACTIONr_mcangle_other1.2832.0731612
X-RAY DIFFRACTIONr_scbond_it0.9311.5251387
X-RAY DIFFRACTIONr_scbond_other0.9291.5181382
X-RAY DIFFRACTIONr_scangle_it1.5142.2272019
X-RAY DIFFRACTIONr_scangle_other1.5142.2282020
X-RAY DIFFRACTIONr_lrange_it3.77127.02111641
X-RAY DIFFRACTIONr_lrange_other3.54626.36411255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.532-1.5720.271580.2473459X-RAY DIFFRACTION89.4633
1.572-1.6150.2171780.2123614X-RAY DIFFRACTION96.4885
1.615-1.6620.2551620.2113574X-RAY DIFFRACTION96.5375
1.662-1.7130.2321630.1983435X-RAY DIFFRACTION97.3222
1.713-1.7690.2451640.1933364X-RAY DIFFRACTION97.6744
1.769-1.8310.2081530.1883238X-RAY DIFFRACTION97.6108
1.831-1.90.2221640.1872929X-RAY DIFFRACTION91.7532
1.9-1.9770.221770.193010X-RAY DIFFRACTION98.0012
1.977-2.0650.2191570.1852925X-RAY DIFFRACTION98.4036
2.065-2.1660.2131350.1862788X-RAY DIFFRACTION98.75
2.166-2.2830.1691150.1782685X-RAY DIFFRACTION98.8352
2.283-2.4210.1941350.1672524X-RAY DIFFRACTION98.9579
2.421-2.5870.2171270.1662298X-RAY DIFFRACTION96.8837
2.587-2.7940.2081100.162068X-RAY DIFFRACTION91.5896
2.794-3.060.2211110.1812029X-RAY DIFFRACTION99.8134
3.06-3.420.18940.1731867X-RAY DIFFRACTION99.8981
3.42-3.9460.149740.1621664X-RAY DIFFRACTION99.5418
3.946-4.8260.164790.1531349X-RAY DIFFRACTION97.0768
4.826-6.7950.191340.2021017X-RAY DIFFRACTION91.5505
6.795-43.5570.17360.204620X-RAY DIFFRACTION99.2436

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