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- PDB-9v7r: The apo structure of HnH6H -

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Basic information

Entry
Database: PDB / ID: 9v7r
TitleThe apo structure of HnH6H
ComponentsHyoscyamine 6-dioxygenase
KeywordsOXIDOREDUCTASE / non-heme oxygenases / hyoscyamine / hydroxylation
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
: / Hyoscyamine 6-dioxygenase
Similarity search - Component
Biological speciesHyoscyamus niger (henbane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45004339752 Å
AuthorsWu, L. / Zhou, J.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The apo structure of HnH6H
Authors: Wu, L. / Zhou, J.H.
History
DepositionMay 28, 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
G: Hyoscyamine 6-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6037
Polymers86,2112
Non-polymers3915
Water2,828157
1
A: Hyoscyamine 6-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3194
Polymers43,1061
Non-polymers2133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Hyoscyamine 6-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2843
Polymers43,1061
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.129, 43.156, 91.465
Angle α, β, γ (deg.)80.769, 87.931, 83.345
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 43105.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyoscyamus niger (henbane) / Gene: H6H / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24397, hyoscyamine (6S)-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES (pH 7.0), 1 M ammonium sulfate and 1 M potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.45→19.82 Å / Num. obs: 23244 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.3501399492 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.047 / Net I/σ(I): 13
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2681 / CC1/2: 0.851 / Rpim(I) all: 0.222 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45004339752→19.8195282064 Å / SU ML: 0.298197054302 / Cross valid method: FREE R-VALUE / σ(F): 1.98740005101 / Phase error: 24.4646654739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238488892933 1176 5.06089426346 %
Rwork0.180359084865 22061 -
obs0.183306733218 23237 97.8358805945 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.2856774551 Å2
Refinement stepCycle: LAST / Resolution: 2.45004339752→19.8195282064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 19 157 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002511944976084908
X-RAY DIFFRACTIONf_angle_d0.5771249648526667
X-RAY DIFFRACTIONf_chiral_restr0.0416180136821734
X-RAY DIFFRACTIONf_plane_restr0.00400898144326858
X-RAY DIFFRACTIONf_dihedral_angle_d15.72206301522977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4500434-2.56130.2869526169711340.2190412705822810X-RAY DIFFRACTION97.7423638778
2.5613-2.69610.3074640587721450.2207125871822789X-RAY DIFFRACTION97.6372712146
2.6961-2.86450.2960297285261550.2167540267312726X-RAY DIFFRACTION97.9931972789
2.8645-3.08490.2631244903931380.2151002532822750X-RAY DIFFRACTION97.9315022041
3.0849-3.3940.2773727156461430.1962377588092762X-RAY DIFFRACTION97.976391231
3.394-3.88190.2408119172961570.1740411801322764X-RAY DIFFRACTION98.4828051247
3.8819-4.87870.1947480345451430.1445872973242748X-RAY DIFFRACTION97.9004402303
4.8787-19.81950.187972547451610.1530030240242712X-RAY DIFFRACTION97.0608108108

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