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- PDB-21ii: Crystal structure of terpeniod cyclase SpSODS in complex with GPP... -

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Basic information

Entry
Database: PDB / ID: 21ii
TitleCrystal structure of terpeniod cyclase SpSODS in complex with GPP and Mg2+
ComponentsTerpene synthase
KeywordsLYASE / terpeniod cyclase / sodorifen synthase / SpSODS
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / GERANYL DIPHOSPHATE / PYROPHOSPHATE 2- / Terpene synthase
Function and homology information
Biological speciesSerratia plymuthica 4Rx13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsLi, X.Q. / Zhang, L.L. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structure and catalytic mechanism of C 16 terpenoid cyclase SpSODS from Serratia plymuthica.
Authors: Li, X. / Zhang, L. / Zheng, Y. / Pan, N. / Zhou, Z. / Huang, Y. / Liang, Q. / Huang, J.W. / Chen, C.C. / Guo, R.T.
History
DepositionDec 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 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: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,27711
Polymers84,5192
Non-polymers7589
Water14,610811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-72 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.968, 92.968, 170.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-1185-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Terpene synthase / Sodorifen synthase SpSODS


Mass: 42259.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism Saccharomyces cerevisiae is not available during the biocuration, replaced by A0A318P116 temporarily.
Source: (gene. exp.) Serratia plymuthica 4Rx13 (bacteria) / Gene: CT690_00725 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A318P116, Lyases; Carbon-oxygen lyases; Acting on phosphates

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Non-polymers , 5 types, 820 molecules

#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% (w/v) PEG 3350, 0.01 M MgCl2, 0.1 M Tris-HCl, pH 8.5

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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: Nov 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 77452 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.028 / Rrim(I) all: 0.133 / Χ2: 0.83 / Net I/σ(I): 6 / Num. measured all: 1565816
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.74-1.818.81.30976220.840.9560.31.3440.47899.9
1.8-1.8718.71.0276090.9070.9750.2321.0470.477100
1.87-1.9618.10.70376410.9610.990.1630.7220.596100
1.96-2.0619.70.43776500.980.9950.0970.4480.51100
2.06-2.1919.10.29476710.9890.9970.0670.3020.57100
2.19-2.3618.10.24476810.9910.9980.0570.250.892100
2.36-2.620.60.15277240.9960.9990.0340.1560.892100
2.6-2.9821.30.11577610.9970.9990.0250.1181.273100
2.98-3.7524.50.09178590.99910.0190.0931.197100
3.75-5022.90.07882340.99810.0170.0791.12299.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→48.47 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 3973 5.15 %
Rwork0.1945 --
obs0.1968 77154 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5832 0 30 811 6673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086010
X-RAY DIFFRACTIONf_angle_d0.9888153
X-RAY DIFFRACTIONf_dihedral_angle_d5.715829
X-RAY DIFFRACTIONf_chiral_restr0.053855
X-RAY DIFFRACTIONf_plane_restr0.0091068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.760.32471290.27692564X-RAY DIFFRACTION100
1.76-1.780.3291470.26312595X-RAY DIFFRACTION100
1.78-1.810.34281450.24182557X-RAY DIFFRACTION100
1.81-1.830.27741330.23462602X-RAY DIFFRACTION100
1.83-1.860.26891270.23162599X-RAY DIFFRACTION100
1.86-1.880.2871410.24122570X-RAY DIFFRACTION100
1.88-1.910.50131330.36462523X-RAY DIFFRACTION98
1.91-1.950.45361470.41062594X-RAY DIFFRACTION100
1.95-1.980.27441540.23542584X-RAY DIFFRACTION100
1.98-2.010.24811560.20532564X-RAY DIFFRACTION100
2.01-2.050.25051430.20252603X-RAY DIFFRACTION100
2.05-2.10.28451410.19472573X-RAY DIFFRACTION100
2.1-2.140.26291460.19742584X-RAY DIFFRACTION100
2.14-2.190.22791450.20172617X-RAY DIFFRACTION100
2.19-2.250.32671420.26872486X-RAY DIFFRACTION97
2.25-2.310.30361400.29152554X-RAY DIFFRACTION98
2.31-2.370.27011310.20252618X-RAY DIFFRACTION100
2.37-2.450.23811580.18792610X-RAY DIFFRACTION100
2.45-2.540.21651440.17332601X-RAY DIFFRACTION100
2.54-2.640.22011310.16932629X-RAY DIFFRACTION100
2.64-2.760.22871470.17472615X-RAY DIFFRACTION100
2.76-2.910.2411390.17792654X-RAY DIFFRACTION100
2.91-3.090.21151230.17722662X-RAY DIFFRACTION100
3.09-3.330.21131510.17112641X-RAY DIFFRACTION100
3.33-3.660.22191390.17022669X-RAY DIFFRACTION100
3.66-4.190.18231500.15162682X-RAY DIFFRACTION100
4.19-5.280.16921480.15532730X-RAY DIFFRACTION100
5.28-48.470.22481430.17952901X-RAY DIFFRACTION100

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