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- PDB-9k9x: Crystal structure of bicyclogermacrene synthase -

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Basic information

Entry
Database: PDB / ID: 9k9x
TitleCrystal structure of bicyclogermacrene synthase
Components(Bicyclogermacrene synthase) x 2
KeywordsLYASE / Terpene synthase / complex with Mg
Function / homology
Function and homology information


bicyclogermacrene synthase / farnesyl diphosphate catabolic process / bicyclogermacrene biosynthetic process / sesquiterpene synthase activity / diterpenoid biosynthetic process / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / : / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Bicyclogermacrene synthase
Similarity search - Component
Biological speciesPhyla dulcis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsTian, B.X. / Fan, S.L. / Chen, X.L. / Guo, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22473067 China
National Natural Science Foundation of China (NSFC)32300055 China
CitationJournal: To Be Published
Title: Enhancing Enzyme Activity with Mutation Combinations Guided by Few-shot Learning and Causal Inference
Authors: Guo, L. / Yan, X.G. / Nie, S.X. / Ge, M.Y. / Li, Y.K. / Lu, Y.L. / Li, W.G. / Zhang, X.C. / Liang, D.M. / Zhao, Y.H. / Tang, H.X. / Chen, X.L. / Fan, S.L. / Tang, Y.F. / Qiao, J.J. / Tian, B.X.
History
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,3504
Polymers131,1612
Non-polymers1902
Water12,881715
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)110.551, 111.703, 238.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Bicyclogermacrene synthase / Terpene synthase 5 / LdTPS5


Mass: 66560.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phyla dulcis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: J7LMP2, bicyclogermacrene synthase
#2: Protein Bicyclogermacrene synthase / Terpene synthase 5 / LdTPS5


Mass: 64600.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phyla dulcis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: J7LMP2, bicyclogermacrene synthase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.48 M Sodium phosphate monobasic monohydrate and 0.68-0.76M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.03→30.63 Å / Num. obs: 92661 / % possible obs: 94.8 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 15.4
Reflection shellResolution: 2.03→2.1 Å / Num. unique obs: 92662 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G4D

3g4d


Resolution: 2.03→30.63 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 1992 2.15 %
Rwork0.184 --
obs0.1845 92661 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8687 0 10 715 9412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.1491171
X-RAY DIFFRACTIONf_chiral_restr0.041281
X-RAY DIFFRACTIONf_plane_restr0.0071549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.33181090.29785344X-RAY DIFFRACTION82
2.14-2.20.26731410.23426372X-RAY DIFFRACTION97
2.2-2.270.25031450.21376458X-RAY DIFFRACTION98
2.27-2.350.21411390.20316534X-RAY DIFFRACTION99
2.35-2.450.26141420.18916583X-RAY DIFFRACTION100
2.45-2.560.24071490.19096550X-RAY DIFFRACTION100
2.56-2.690.19951440.18256607X-RAY DIFFRACTION100
2.69-2.860.21391480.18096605X-RAY DIFFRACTION100
2.86-3.080.19761460.18336595X-RAY DIFFRACTION100
3.08-3.390.20791430.1746650X-RAY DIFFRACTION100
3.39-3.880.18461420.15996662X-RAY DIFFRACTION100
3.88-4.890.16551510.15256731X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0260.2570.37761.3401-0.61152.357-0.04480.11330.061-0.0154-0.0564-0.0034-0.1994-0.020.08880.22290.0502-0.02370.2316-0.03770.187-25.2925-30.508-59.8147
20.3635-0.06050.04481.0512-0.44253.20160.0446-0.0102-0.02550.1261-0.06980.0555-0.02160.05220.02460.1426-0.005-0.0260.1608-0.02970.1974-19.6874-40.6656-30.4556
31.3199-0.18590.19282.6422-0.10352.09280.0394-0.02-0.04110.0383-0.03040.4118-0.1796-0.3653-0.01220.2590.0448-0.03280.2916-0.01770.2364-31.4582-33.0374-42.8877
40.4224-0.0272-0.21090.3416-0.06781.05-0.0752-0.0537-0.0411-0.00490.02250.03450.0444-0.0190.05370.23670.0209-0.00910.1798-0.01980.2291-21.6593-23.117616.5243
50.28930.3196-0.62591.41290.13032.1572-0.04140.09830.0309-0.0347-0.01550.34610.0966-0.44070.04670.2744-0.0049-0.03980.297-0.0150.3063-29.1207-24.18424.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 238 )
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 436 )
3X-RAY DIFFRACTION3chain 'A' and (resid 437 through 565 )
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 374 )
5X-RAY DIFFRACTION5chain 'B' and (resid 375 through 565 )

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