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- PDB-21ih: Crystal structure of terpeniod cyclase SpSODS in complex with PPi... -

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Basic information

Entry
Database: PDB / ID: 21ih
TitleCrystal structure of terpeniod cyclase SpSODS in complex with PPi 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 / PYROPHOSPHATE 2- / Terpene synthase
Function and homology information
Biological speciesSerratia plymuthica 4Rx13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 15, 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)85,13911
Polymers84,5192
Non-polymers6209
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-68 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.888, 92.888, 170.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Terpene synthase / Sodorifen synthase SpSODS


Mass: 42259.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#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-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: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.24 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% (w/v) PEG 4000, 0.1 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: NSRRC / Beamline: TPS 07A / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 61050 / % possible obs: 98 % / Redundancy: 6.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Χ2: 0.877 / Net I/σ(I): 9.8 / Num. measured all: 404243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.87-1.947.20.68861130.8360.9540.2670.7410.4899.6
1.94-2.017.30.4760880.9130.9770.180.5050.52299.6
2.01-2.117.20.3160980.9540.9880.120.3340.58799.4
2.11-2.227.10.20760950.9780.9940.080.2230.67899.2
2.22-2.366.90.14360570.9860.9960.0570.1550.84498.5
2.36-2.546.60.10460240.9920.9980.0430.1131.0397.5
2.54-2.796.20.07960400.9940.9980.0330.0861.28597.2
2.79-3.25.90.06160880.9960.9990.0270.0671.25497.3
3.2-4.035.50.04761070.9970.9990.0220.0521.1396.8
4.03-506.30.0463400.99810.0170.0441.24195.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→27.19 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 3025 4.96 %RANDOM
Rwork0.1921 ---
obs0.1941 61008 97.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→27.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5835 0 20 366 6221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086003
X-RAY DIFFRACTIONf_angle_d1.0158145
X-RAY DIFFRACTIONf_dihedral_angle_d10.129821
X-RAY DIFFRACTIONf_chiral_restr0.054855
X-RAY DIFFRACTIONf_plane_restr0.0091066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.35261280.28192537X-RAY DIFFRACTION96
1.9-1.930.3931320.26382644X-RAY DIFFRACTION100
1.93-1.960.27051310.26782642X-RAY DIFFRACTION99
1.96-20.32481330.25772627X-RAY DIFFRACTION100
2-2.040.29511350.25352648X-RAY DIFFRACTION100
2.04-2.080.2971420.24052637X-RAY DIFFRACTION99
2.08-2.120.30651460.23322613X-RAY DIFFRACTION99
2.13-2.170.27551520.2342628X-RAY DIFFRACTION99
2.17-2.230.27681370.22012626X-RAY DIFFRACTION99
2.23-2.290.25041330.21722625X-RAY DIFFRACTION99
2.29-2.360.26491410.2162639X-RAY DIFFRACTION98
2.36-2.430.25321340.21192599X-RAY DIFFRACTION98
2.43-2.520.24551600.19612572X-RAY DIFFRACTION97
2.52-2.620.25121470.20512606X-RAY DIFFRACTION98
2.62-2.740.26191240.20522628X-RAY DIFFRACTION97
2.74-2.880.2511240.20492619X-RAY DIFFRACTION97
2.88-3.060.23911580.20922604X-RAY DIFFRACTION97
3.06-3.30.27311200.19932680X-RAY DIFFRACTION97
3.3-3.630.20641420.18772632X-RAY DIFFRACTION97
3.63-4.160.22431560.16532636X-RAY DIFFRACTION96
4.16-5.230.18651140.16552651X-RAY DIFFRACTION94
5.23-27.190.19211360.16862890X-RAY DIFFRACTION98

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