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- PDB-8cvc: Structure of Hyoscyamine 6-beta Hydroxylase in complex with vanad... -

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Basic information

Entry
Database: PDB / ID: 8cvc
TitleStructure of 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 / OXYGEN ATOM / 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: 1.791 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: To Be Published
Title: Structure mimicking the H6H cyclization ferryl complex
Authors: Wenger, E.S. / Boal, A.K. / Bollinger, J.M. / Krebs, C.
History
DepositionMay 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: 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-beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,85318
Polymers42,6331
Non-polymers1,22017
Water4,684260
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)44.911, 79.761, 56.187
Angle α, β, γ (deg.)90.000, 111.054, 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 , 8 types, 277 molecules

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


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


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#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-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.: 260 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.72 % / 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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 34735 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.889 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.026 / Net I/σ(I): 24.4
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1754 / CC1/2: 0.889 / Rpim(I) all: 0.199 / % possible all: 100

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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: 1.791→40.654 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.134 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1943 1839 5.294 %
Rwork0.1729 32896 -
all0.174 --
obs-34735 99.716 %
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: 20.243 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å2-0.001 Å2
2--0.002 Å20 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.791→40.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 70 260 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132727
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172575
X-RAY DIFFRACTIONr_angle_refined_deg1.21.6523692
X-RAY DIFFRACTIONr_angle_other_deg1.1861.5785984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75125.039129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.377157
X-RAY DIFFRACTIONr_chiral_restr0.0570.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02558
X-RAY DIFFRACTIONr_nbd_refined0.1890.2492
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.22250
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21306
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2215
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1380.29
X-RAY DIFFRACTIONr_nbd_other0.1210.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0710.23
X-RAY DIFFRACTIONr_mcbond_it1.0691.9961313
X-RAY DIFFRACTIONr_mcbond_other1.0681.9981314
X-RAY DIFFRACTIONr_mcangle_it1.8642.9841640
X-RAY DIFFRACTIONr_mcangle_other1.8642.9851641
X-RAY DIFFRACTIONr_scbond_it1.2612.1971414
X-RAY DIFFRACTIONr_scbond_other1.2612.1981415
X-RAY DIFFRACTIONr_scangle_it2.1023.2032051
X-RAY DIFFRACTIONr_scangle_other2.1023.2042052
X-RAY DIFFRACTIONr_lrange_it3.95124.7093026
X-RAY DIFFRACTIONr_lrange_other3.87524.2732962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.791-1.8370.2481340.2252331X-RAY DIFFRACTION96.3643
1.837-1.8880.2311390.2022363X-RAY DIFFRACTION100
1.888-1.9420.2271480.1922306X-RAY DIFFRACTION100
1.942-2.0020.2171290.1882217X-RAY DIFFRACTION100
2.002-2.0680.2151260.1872162X-RAY DIFFRACTION100
2.068-2.140.2131310.1742097X-RAY DIFFRACTION100
2.14-2.2210.1891090.1822011X-RAY DIFFRACTION100
2.221-2.3110.181030.1671953X-RAY DIFFRACTION100
2.311-2.4140.2191060.1671873X-RAY DIFFRACTION100
2.414-2.5310.188940.1691789X-RAY DIFFRACTION100
2.531-2.6680.2121200.1711686X-RAY DIFFRACTION100
2.668-2.8290.1891020.1641584X-RAY DIFFRACTION100
2.829-3.0240.22580.1781548X-RAY DIFFRACTION100
3.024-3.2650.219530.181453X-RAY DIFFRACTION100
3.265-3.5750.197670.1751292X-RAY DIFFRACTION100
3.575-3.9950.153750.1581179X-RAY DIFFRACTION100
3.995-4.6090.153440.141060X-RAY DIFFRACTION100
4.609-5.6340.173470.162900X-RAY DIFFRACTION100
5.634-7.9220.159380.184688X-RAY DIFFRACTION100
7.922-40.6540.201160.177404X-RAY DIFFRACTION98.5915

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