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- PDB-7wat: The Crystal Structure of Bifunctional Miltiradiene Synthase from ... -

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Basic information

Entry
Database: PDB / ID: 7wat
TitleThe Crystal Structure of Bifunctional Miltiradiene Synthase from Selaginella moellendorffii
ComponentsBifunctional diterpene synthase
KeywordsPLANT PROTEIN / bifunctional terpene synthase / GGPP / CPP / miltiradiene
Function / homology
Function and homology information


miltiradiene synthase / miltiradiene synthase activity / miltiradiene biosynthetic process / 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate catabolic process / 5alpha,9alpha,10beta-labda-8(20),13-dien-15-yl diphosphate biosynthetic process / copalyl diphosphate synthase activity / copalyl diphosphate synthase / diterpenoid biosynthetic process / terpene synthase activity / chloroplast / magnesium ion binding
Similarity search - Function
Glycosyltransferase - #160 / Terpene synthase, metal-binding domain / 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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Glycosyltransferase - #160 / Terpene synthase, metal-binding domain / 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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional diterpene synthase, chloroplastic
Similarity search - Component
Biological speciesSelaginella moellendorffii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMa, X. / Tong, Y. / Jiang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670750 China
CitationJournal: Plant Biotechnol J / Year: 2023
Title: Structural and mechanistic insights into the precise product synthesis by a bifunctional miltiradiene synthase.
Authors: Tong, Y. / Ma, X. / Hu, T. / Chen, K. / Cui, G. / Su, P. / Xu, H. / Gao, W. / Jiang, T. / Huang, L.
History
DepositionDec 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Bifunctional diterpene synthase


Theoretical massNumber of molelcules
Total (without water)91,5421
Polymers91,5421
Non-polymers00
Water7,152397
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33210 Å2
Unit cell
Length a, b, c (Å)55.788, 83.530, 192.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Bifunctional diterpene synthase / Copalyl diphosphate synthase / Miltiradiene synthase / SmMDS / Terpene synthase 4 / SmTPS4


Mass: 91542.477 Da / Num. of mol.: 1 / Mutation: A136P, L264I, D314G, P409T, R632K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: MDS
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G9MAN7, copalyl diphosphate synthase, miltiradiene synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES (pH 6.5) 22% (v/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 57086 / % possible obs: 93.01 % / Redundancy: 7.4 % / Biso Wilson estimate: 35.99 Å2 / Rrim(I) all: 0.172 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 5031 / Rpim(I) all: 0.663

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S9V

3s9v


Resolution: 2→48.24 Å / SU ML: 0.2568 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.9857 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 1999 3.5 %
Rwork0.1928 55038 -
obs0.1941 57037 93.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.27 Å2
Refinement stepCycle: LAST / Resolution: 2→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 0 397 6672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716429
X-RAY DIFFRACTIONf_angle_d0.81928714
X-RAY DIFFRACTIONf_chiral_restr0.0454961
X-RAY DIFFRACTIONf_plane_restr0.00561101
X-RAY DIFFRACTIONf_dihedral_angle_d19.91642367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35421240.31713411X-RAY DIFFRACTION81.53
2.05-2.110.31051330.27883638X-RAY DIFFRACTION88.4
2.11-2.170.29071340.24313696X-RAY DIFFRACTION88.53
2.17-2.240.33191350.22613705X-RAY DIFFRACTION88.56
2.24-2.320.21471360.21573755X-RAY DIFFRACTION89.22
2.32-2.410.25671380.2043797X-RAY DIFFRACTION91.36
2.41-2.520.25721390.1973829X-RAY DIFFRACTION90.97
2.52-2.660.23781410.19253920X-RAY DIFFRACTION93.68
2.66-2.820.23721480.19354039X-RAY DIFFRACTION96.25
2.82-3.040.2631490.19434123X-RAY DIFFRACTION97.56
3.04-3.350.25091510.19214145X-RAY DIFFRACTION97.48
3.35-3.830.20931530.17534219X-RAY DIFFRACTION99.34
3.83-4.830.19811560.15634298X-RAY DIFFRACTION99.53
4.83-48.240.20321620.20174463X-RAY DIFFRACTION98.95

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