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- PDB-9ka1: Crystal structure of bicyclogermacrene synthase mutant I290V/I385... -

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Basic information

Entry
Database: PDB / ID: 9ka1
TitleCrystal structure of bicyclogermacrene synthase mutant I290V/I385C/V434C/L454C/V476W/L558I
ComponentsBicyclogermacrene synthase
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
Bicyclogermacrene synthase
Similarity search - Component
Biological speciesPhyla dulcis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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


Theoretical massNumber of molelcules
Total (without water)133,2352
Polymers133,2352
Non-polymers00
Water4,089227
1
A: Bicyclogermacrene synthase


Theoretical massNumber of molelcules
Total (without water)66,6171
Polymers66,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bicyclogermacrene synthase


Theoretical massNumber of molelcules
Total (without water)66,6171
Polymers66,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.335, 90.939, 233.974
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 Bicyclogermacrene synthase / Terpene synthase 5 / LdTPS5


Mass: 66617.406 Da / Num. of mol.: 2 / Mutation: I290V,I385C,V434C,L454C,V476W,L558I
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 15% PEG4000, 0.1M Na Citrate pH 5.4, 0.2M NaAC

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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 EIGER2 X 9M / Detector: PIXEL / Date: Jun 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→31.37 Å / Num. obs: 53920 / % possible obs: 95.55 % / Redundancy: 6 % / CC1/2: 0.972 / Net I/σ(I): 9.57
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 53844 / CC1/2: 0.972

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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: 2.3→31.37 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1995 3.7 %
Rwork0.217 --
obs0.2182 53867 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8461 0 0 227 8688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d5.1871138
X-RAY DIFFRACTIONf_chiral_restr0.0421246
X-RAY DIFFRACTIONf_plane_restr0.0071514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.37061150.29282973X-RAY DIFFRACTION78
2.36-2.420.32181230.29153193X-RAY DIFFRACTION84
2.42-2.490.32071270.28273335X-RAY DIFFRACTION87
2.49-2.570.32581370.28193541X-RAY DIFFRACTION92
2.57-2.660.33191430.27513753X-RAY DIFFRACTION97
2.66-2.770.31671480.25863821X-RAY DIFFRACTION99
2.77-2.90.3121470.24913814X-RAY DIFFRACTION99
2.9-3.050.28881480.24043829X-RAY DIFFRACTION100
3.05-3.240.25051490.23243870X-RAY DIFFRACTION100
3.24-3.490.23441490.21853867X-RAY DIFFRACTION100
3.49-3.840.23721470.19863876X-RAY DIFFRACTION100
3.84-4.390.20181500.17873908X-RAY DIFFRACTION100
4.39-5.530.19741530.18083952X-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)
11.30050.13060.49621.8085-0.19392.1884-0.1802-0.03880.26910.00970.0041-0.0127-0.28050.04630.18820.3377-0.0548-0.05540.26290.00390.2446-16.1706-1.151140.4801
20.6192-0.26050.38970.80410.0153.36060.10070.12790.0187-0.1914-0.1181-0.03230.4124-0.0153-0.01790.2448-0.02280.01870.20160.00220.2116-22.4222-14.387510.7939
30.55510.84820.7752.7062-0.18782.14160.01320.2532-0.19850.1688-0.1526-0.5666-0.34910.66940.09440.4833-0.0731-0.00110.51670.05850.4163-14.11772.408516.9929
40.964-0.62720.43522.11370.39721.348-0.0773-0.11680.1040.16550.0865-0.1876-0.06050.15030.04620.348-0.0115-0.00620.30020.03320.2532-15.3684-9.003426.6026
52.08050.50780.7772.06920.54972.3167-0.2113-0.16840.2369-0.18960.02420.3102-0.3253-0.14570.16190.33070.0352-0.050.2340.06420.26342.4797-42.818944.2994
61.788-0.1364-0.83372.9646-0.50252.163-0.1599-0.1381-0.00820.1295-0.084-0.5518-0.14430.64430.20670.3191-0.0708-0.05740.41340.05260.288825.3446-46.346447.3336
70.526-0.1320.03090.5426-0.00310.8-0.19440.0448-0.1448-0.14530.19710.25640.3492-0.2908-0.0670.2838-0.0132-0.0820.30220.0540.24919.9269-53.416248.2217
80.68730.0263-0.00740.6144-0.57693.3425-0.00070.0439-0.0523-0.3055-0.0162-0.0377-0.0331-0.18880.01170.3039-0.0414-0.03620.1958-0.00140.2787-3.4946-51.678517.8042
91.56780.68961.3180.49040.1962.00930.05440.3208-0.243-0.31630.0544-0.1891-0.18910.5547-0.02660.4822-0.05690.03550.47680.00570.316315.3951-47.589422.0912
101.49781.02560.45131.40570.06661.07960.0343-0.0652-0.11790.1261-0.08290.0668-0.1470.0116-0.00970.3963-0.028-0.00530.25120.05190.31435.4811-52.367833.3703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 238 )
2X-RAY DIFFRACTION2chain 'A' and (resid 239 through 401 )
3X-RAY DIFFRACTION3chain 'A' and (resid 402 through 512 )
4X-RAY DIFFRACTION4chain 'A' and (resid 513 through 565 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 132 )
6X-RAY DIFFRACTION6chain 'B' and (resid 133 through 197 )
7X-RAY DIFFRACTION7chain 'B' and (resid 198 through 238 )
8X-RAY DIFFRACTION8chain 'B' and (resid 239 through 398 )
9X-RAY DIFFRACTION9chain 'B' and (resid 399 through 512 )
10X-RAY DIFFRACTION10chain 'B' and (resid 513 through 565 )

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