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- PDB-8cvb: Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron,... -

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Basic information

Entry
Database: PDB / ID: 8cvb
TitleStructure of 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: 1.532 Å
AuthorsWenger, E.W. / 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

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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)44,04020
Polymers42,6331
Non-polymers1,40719
Water5,603311
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)44.801, 79.329, 55.848
Angle α, β, γ (deg.)90.000, 110.994, 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 , 7 types, 330 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / 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.: 311 / 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: 42.95 % / 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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2020
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 54702 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.93 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Net I/σ(I): 34.8
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 5 / Num. unique obs: 2733 / CC1/2: 0.93 / Rpim(I) all: 0.157 / % possible all: 99

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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→43.61 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.222 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2037 2694 4.925 %
Rwork0.1826 52008 -
all0.184 --
obs-54702 99.914 %
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: 14.553 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å2-0 Å2-0.001 Å2
2--0.003 Å2-0 Å2
3----0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.532→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 82 311 2971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132705
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172569
X-RAY DIFFRACTIONr_angle_refined_deg1.151.6563652
X-RAY DIFFRACTIONr_angle_other_deg1.2011.5785962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.524.803127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03315456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.667157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_nbd_refined0.1960.2481
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.22328
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21277
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2263
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.29
X-RAY DIFFRACTIONr_nbd_other0.1240.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.211
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0740.23
X-RAY DIFFRACTIONr_mcbond_it0.7061.4011297
X-RAY DIFFRACTIONr_mcbond_other0.7051.4041298
X-RAY DIFFRACTIONr_mcangle_it1.2732.0951616
X-RAY DIFFRACTIONr_mcangle_other1.2722.0961617
X-RAY DIFFRACTIONr_scbond_it0.8361.5561408
X-RAY DIFFRACTIONr_scbond_other0.8361.5531407
X-RAY DIFFRACTIONr_scangle_it1.3722.2482036
X-RAY DIFFRACTIONr_scangle_other1.3722.2512037
X-RAY DIFFRACTIONr_lrange_it4.1717.8663034
X-RAY DIFFRACTIONr_lrange_other3.93717.1522934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.532-1.5720.2352180.2143757X-RAY DIFFRACTION99.0284
1.572-1.6150.2122150.1953736X-RAY DIFFRACTION100
1.615-1.6620.2692050.2033636X-RAY DIFFRACTION100
1.662-1.7130.2111690.1983509X-RAY DIFFRACTION100
1.713-1.7690.221600.1933425X-RAY DIFFRACTION100
1.769-1.8310.2031680.1933331X-RAY DIFFRACTION100
1.831-1.90.2121830.1913183X-RAY DIFFRACTION100
1.9-1.9770.2221470.1953092X-RAY DIFFRACTION100
1.977-2.0650.1981560.1852970X-RAY DIFFRACTION100
2.065-2.1660.1841560.1832808X-RAY DIFFRACTION100
2.166-2.2830.1951300.1792681X-RAY DIFFRACTION99.9644
2.283-2.4210.187980.1782587X-RAY DIFFRACTION100
2.421-2.5870.2011090.1792388X-RAY DIFFRACTION100
2.587-2.7940.1851400.1812246X-RAY DIFFRACTION100
2.794-3.060.2151060.192033X-RAY DIFFRACTION100
3.06-3.420.207930.1781865X-RAY DIFFRACTION100
3.42-3.9460.206730.1681657X-RAY DIFFRACTION100
3.946-4.8260.141630.1521414X-RAY DIFFRACTION100
4.826-6.7960.212610.181078X-RAY DIFFRACTION100
6.796-43.610.26440.189612X-RAY DIFFRACTION99.0937

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