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- PDB-9v6v: The complex structure of HnH6H and 6-hydroxyhyoscyamine -

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Basic information

Entry
Database: PDB / ID: 9v6v
TitleThe complex structure of HnH6H and 6-hydroxyhyoscyamine
ComponentsHyoscyamine 6-dioxygenase
KeywordsOXIDOREDUCTASE / oxygenases / 6-hydroxyhyoscyamine / epoxidation
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 / : / Chem-OVR / Hyoscyamine 6-dioxygenase
Similarity search - Component
Biological speciesHyoscyamus niger (henbane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70001021544 Å
AuthorsWu, L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The complex structure of HnH6H and 6-hydroxyhyoscyamine
Authors: Wu, L. / Zhou, J.H.
History
DepositionMay 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hyoscyamine 6-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7416
Polymers43,1061
Non-polymers6355
Water5,459303
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)43.369, 80.045, 48.231
Angle α, β, γ (deg.)90.000, 97.454, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hyoscyamine 6-dioxygenase / Hyoscyamine 6-beta-hydroxylase


Mass: 43105.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyoscyamus niger (henbane) / Gene: H6H / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P24397, hyoscyamine (6S)-dioxygenase

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Non-polymers , 6 types, 308 molecules

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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH6.5, 0.2 M Magnesium chloride, 25%pEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.7→19.38 Å / Num. obs: 35949 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.3640019067 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Net I/σ(I): 22.7
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.211 / Num. unique obs: 1957 / CC1/2: 0.977 / Rpim(I) all: 0.126

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.70001021544→19.38 Å / SU ML: 0.160089460066 / Cross valid method: FREE R-VALUE / σ(F): 1.36417770229 / Phase error: 17.7754829421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.190486893674 1824 5.07724425887 %
Rwork0.163529166678 34101 -
obs0.164896370691 35925 99.9471399955 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.8763011362 Å2
Refinement stepCycle: LAST / Resolution: 1.70001021544→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 40 303 2863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006548497383632677
X-RAY DIFFRACTIONf_angle_d0.8700458314033651
X-RAY DIFFRACTIONf_chiral_restr0.0551832903151400
X-RAY DIFFRACTIONf_plane_restr0.00593987251801478
X-RAY DIFFRACTIONf_dihedral_angle_d15.4315527751621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.70001022-1.74590.2265705080441380.1851616527362615X-RAY DIFFRACTION100
1.7459-1.79730.2183371415431230.1769197000132646X-RAY DIFFRACTION99.9278238903
1.7973-1.85530.2331580835231420.1773504742512612X-RAY DIFFRACTION99.9637023593
1.8553-1.92150.2108907971061280.168301961972599X-RAY DIFFRACTION99.9633431085
1.9215-1.99840.2153841368791710.1670445012982595X-RAY DIFFRACTION100
1.9984-2.08920.1794442189761400.1565481723492636X-RAY DIFFRACTION99.9639899172
2.0892-2.19920.1949215802641660.1623346781452578X-RAY DIFFRACTION99.9271667881
2.1992-2.33680.2052720393481340.1573619013772625X-RAY DIFFRACTION100
2.3368-2.51690.2293324197061290.1772226374732639X-RAY DIFFRACTION99.9277978339
2.5169-2.76950.1916457709971240.1740371038832629X-RAY DIFFRACTION100
2.7695-3.16870.2097687493391390.1690484730442621X-RAY DIFFRACTION99.8552821997
3.1687-3.98660.1654614852481370.1487752991622651X-RAY DIFFRACTION99.9283154122
3.9866-19.380.1560741975441530.1572405500172655X-RAY DIFFRACTION99.8577524893

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