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- PDB-8jw3: The crystal structure of the viral terpene synthase from Orpheovi... -

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Basic information

Entry
Database: PDB / ID: 8jw3
TitleThe crystal structure of the viral terpene synthase from Orpheovirus IHUMI-LCC2
ComponentsTerpenoid synthase
KeywordsLYASE / Terpene synthase
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Terpenoid synthase
Function and homology information
Biological speciesOrpheovirus IHUMI-LCC2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsJung, Y. / Mitsuhashi, T. / Senda, M. / Sato, S. / Senda, T. / Fujita, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101001 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05461 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Function and Structure of a Terpene Synthase Encoded in a Giant Virus Genome.
Authors: Jung, Y. / Mitsuhashi, T. / Sato, S. / Senda, M. / Senda, T. / Fujita, M.
History
DepositionJun 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terpenoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0014
Polymers37,7131
Non-polymers2883
Water3,999222
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)113.442, 46.763, 69.210
Angle α, β, γ (deg.)90.000, 116.341, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Terpenoid synthase


Mass: 37712.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orpheovirus IHUMI-LCC2 / Gene: ORPV_882 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2I2L5I9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 43.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Citric acid buffer pH 4.5, 1.3 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→42.48 Å / Num. obs: 57694 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.06 Å2 / Rpim(I) all: 0.023 / Net I/σ(I): 18.7
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2840 / Rpim(I) all: 0.366

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se substituted OILTS

Resolution: 1.45→42.48 Å / SU ML: 0.1473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1929 2912 5.05 %
Rwork0.1768 54766 -
obs0.1776 57678 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.84 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 15 222 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552315
X-RAY DIFFRACTIONf_angle_d0.83813157
X-RAY DIFFRACTIONf_chiral_restr0.0716331
X-RAY DIFFRACTIONf_plane_restr0.0089400
X-RAY DIFFRACTIONf_dihedral_angle_d4.509306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.28961210.25122612X-RAY DIFFRACTION99.74
1.47-1.50.25481270.22722602X-RAY DIFFRACTION99.78
1.5-1.530.23511340.22492579X-RAY DIFFRACTION99.89
1.53-1.560.25831240.20922614X-RAY DIFFRACTION99.67
1.56-1.590.22651390.20752593X-RAY DIFFRACTION99.71
1.59-1.620.22711350.1982608X-RAY DIFFRACTION99.85
1.62-1.660.22441410.18452579X-RAY DIFFRACTION99.13
1.66-1.70.2121440.17882596X-RAY DIFFRACTION99.85
1.7-1.750.20531430.18182560X-RAY DIFFRACTION99.89
1.75-1.80.24471240.1782648X-RAY DIFFRACTION99.96
1.8-1.860.18481320.17242612X-RAY DIFFRACTION99.93
1.86-1.920.21281510.17862602X-RAY DIFFRACTION99.96
1.92-20.19581350.17832577X-RAY DIFFRACTION99.96
2-2.090.13171600.16572595X-RAY DIFFRACTION99.93
2.09-2.20.19261430.16792611X-RAY DIFFRACTION99.75
2.2-2.340.18271390.17692601X-RAY DIFFRACTION99.35
2.34-2.520.19251520.1742589X-RAY DIFFRACTION99.89
2.52-2.770.21741380.18492638X-RAY DIFFRACTION99.93
2.77-3.170.16831540.18182599X-RAY DIFFRACTION99.82
3.17-40.19141550.16412637X-RAY DIFFRACTION99.64
4-42.480.1811210.16552714X-RAY DIFFRACTION98.78

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