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- PDB-9kqw: eudesmanediol synthase complexed with Mg2+,PPi and BTAC(PeTS3 complex) -

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Basic information

Entry
Database: PDB / ID: 9kqw
Titleeudesmanediol synthase complexed with Mg2+,PPi and BTAC(PeTS3 complex)
ComponentsTerpenoid synthase
KeywordsLYASE / terpene synthase / eudesmanediol / PPi / BTAC
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE 2- / Terpenoid synthase
Function and homology information
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHuang, Z.Y. / Li, W.L. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2019YFA0905000 China
CitationJournal: To Be Published
Title: The First Microbial Dihydroxylated Terpene Synthase: Structure and Catalytic Mechanism
Authors: Huang, Z.Y. / Li, W.L. / Xu, J.H.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terpenoid synthase
B: Terpenoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,29412
Polymers75,4122
Non-polymers88210
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-66 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.370, 119.460, 123.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Terpenoid synthase


Mass: 37705.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium expansum (fungus) / Gene: PEX2_005160 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A2JK86
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5%(w/V) PEG 4K, 20%(v/v) 1,2,6-hexanetriol, 0.1 M MOPSO/bis-tris pH 6.5; 1 mM rubidium chloride, 1 mM strontium acetate, 1 mM cesium acetate, 1 mM barium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.99→53.76 Å / Num. obs: 60003 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 1.99→2.04 Å / Num. unique obs: 4371 / CC1/2: 0.581

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: 000)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→53.76 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 2002 3.34 %
Rwork0.1905 --
obs0.1917 59919 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 52 456 5595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085271
X-RAY DIFFRACTIONf_angle_d0.9197128
X-RAY DIFFRACTIONf_dihedral_angle_d5.857709
X-RAY DIFFRACTIONf_chiral_restr0.048760
X-RAY DIFFRACTIONf_plane_restr0.01919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.35611370.3144074X-RAY DIFFRACTION100
2.04-2.090.3211450.27794099X-RAY DIFFRACTION100
2.09-2.160.2971300.25114072X-RAY DIFFRACTION100
2.16-2.230.28211500.23744075X-RAY DIFFRACTION100
2.23-2.310.26931410.23194085X-RAY DIFFRACTION100
2.31-2.40.28911410.2184087X-RAY DIFFRACTION100
2.4-2.510.25191430.21254121X-RAY DIFFRACTION100
2.51-2.640.21681440.20044113X-RAY DIFFRACTION100
2.64-2.80.24891350.19944127X-RAY DIFFRACTION100
2.8-3.020.23231420.20424157X-RAY DIFFRACTION100
3.02-3.330.20881450.19164137X-RAY DIFFRACTION100
3.33-3.810.22271420.18374160X-RAY DIFFRACTION100
3.81-4.790.19651510.15534230X-RAY DIFFRACTION100
4.8-53.760.20231560.16134380X-RAY DIFFRACTION100

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