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- PDB-8jmr: Crystal structure of hinokiresinol synthase in complex with 1,7-b... -

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Basic information

Entry
Database: PDB / ID: 8jmr
TitleCrystal structure of hinokiresinol synthase in complex with 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one
Components
  • Hinokiresinol synthase alpha subunit
  • Hinokiresinol synthase beta subunit
KeywordsBIOSYNTHETIC PROTEIN / hinokiresinol / hinokiresinol synthase
Function / homology: / Phloem protein 2-like / Phloem protein 2 / carbohydrate binding / 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one / Hinokiresinol synthase alpha subunit / Hinokiresinol synthase beta subunit
Function and homology information
Biological speciesAsparagus officinalis (garden asparagus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDing, Y. / Ushimaru, R. / Mori, T. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Structural and Mechanistic Insights into the C-C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase.
Authors: Ushimaru, R. / Ding, Y. / Mori, T. / Miyamoto, K. / Uchiyama, M. / Abe, I.
History
DepositionJun 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hinokiresinol synthase alpha subunit
B: Hinokiresinol synthase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7794
Polymers42,3892
Non-polymers3902
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-47 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.831, 103.831, 103.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein Hinokiresinol synthase alpha subunit


Mass: 20176.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asparagus officinalis (garden asparagus)
Gene: AoHRSa / Production host: Escherichia coli (E. coli) / References: UniProt: A9CQD3
#2: Protein Hinokiresinol synthase beta subunit


Mass: 22212.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asparagus officinalis (garden asparagus)
Gene: AoHRSb / Production host: Escherichia coli (E. coli) / References: UniProt: A9CQD5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UR0 / 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one


Mass: 294.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM sodium cacodylate trihydrate (pH6.5), 200mM ammonium sulfate, 20% PEG 8000, 2mM inhibitor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.43 Å / Num. obs: 19260 / % possible obs: 100 % / Redundancy: 22.4 % / Biso Wilson estimate: 28.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.243 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1668 / CC1/2: 0.891

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.43 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.2952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.219 1923 10 %
Rwork0.1708 17313 -
obs0.1755 19236 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.97 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 27 198 2875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562745
X-RAY DIFFRACTIONf_angle_d0.80773723
X-RAY DIFFRACTIONf_chiral_restr0.0532413
X-RAY DIFFRACTIONf_plane_restr0.0056475
X-RAY DIFFRACTIONf_dihedral_angle_d7.0242371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.2811430.20111251X-RAY DIFFRACTION100
2.26-2.320.28751310.1951184X-RAY DIFFRACTION100
2.32-2.380.24481360.19851226X-RAY DIFFRACTION100
2.38-2.460.24341370.2031234X-RAY DIFFRACTION100
2.46-2.550.2631320.19041217X-RAY DIFFRACTION100
2.55-2.650.2631360.18791218X-RAY DIFFRACTION100
2.65-2.770.21491360.19061226X-RAY DIFFRACTION100
2.77-2.920.22871370.20111218X-RAY DIFFRACTION100
2.92-3.10.21451410.17671237X-RAY DIFFRACTION100
3.1-3.340.21761340.16841234X-RAY DIFFRACTION100
3.34-3.680.19851400.15951245X-RAY DIFFRACTION100
3.68-4.210.21011340.14851258X-RAY DIFFRACTION100
4.21-5.30.1761390.13141254X-RAY DIFFRACTION100
5.31-46.430.21691470.18261311X-RAY DIFFRACTION99.93

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