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- PDB-8zgv: Drimenyl diphosphate synthase SsDMS_F248A&D303E from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 8zgv
TitleDrimenyl diphosphate synthase SsDMS_F248A&D303E from Streptomyces showdoensis in complex with farnesyl diphosphate (FPP) and Mg2+
ComponentsSqualene cyclase C-terminal domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / Terpene synthases / type II TSs
Function / homologySqualene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Isomerases; Intramolecular transferases; Transferring other groups / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / isomerase activity / metal ion binding / FARNESYL DIPHOSPHATE / Drimenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces showdoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPan, X.M. / Dong, S.M. / Dong, L.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: To Be Published
Title: Catalytic bases in class II terpene cyclases
Authors: Pan, X.M. / Dong, S.M. / Dong, L.B.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Squalene cyclase C-terminal domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9744
Polymers57,5431
Non-polymers4313
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The gel filtration suggested the protein is a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.480, 114.120, 180.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Squalene cyclase C-terminal domain-containing protein


Mass: 57542.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: F248A,D303E / Source: (gene. exp.) Streptomyces showdoensis (bacteria) / Gene: VO63_21045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2P2GK84
#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.32 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→90.37 Å / Num. obs: 49641 / % possible obs: 99.6 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 7000 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.25 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2092 2000 4.04 %
Rwork0.1834 --
obs0.1844 49520 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 26 506 4082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.075
X-RAY DIFFRACTIONf_dihedral_angle_d14.6481338
X-RAY DIFFRACTIONf_chiral_restr0.07556
X-RAY DIFFRACTIONf_plane_restr0.012663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.28931340.22453201X-RAY DIFFRACTION94
1.85-1.890.25291420.20273353X-RAY DIFFRACTION99
1.89-1.950.23731390.20283332X-RAY DIFFRACTION100
1.95-2.010.23311430.19083384X-RAY DIFFRACTION100
2.01-2.090.22621420.18253388X-RAY DIFFRACTION100
2.09-2.170.20841430.16823368X-RAY DIFFRACTION100
2.17-2.270.21351410.18543365X-RAY DIFFRACTION100
2.27-2.390.21131430.17463406X-RAY DIFFRACTION100
2.39-2.540.2441420.18733394X-RAY DIFFRACTION100
2.54-2.730.22381440.193425X-RAY DIFFRACTION100
2.73-3.010.22231460.19953433X-RAY DIFFRACTION100
3.01-3.440.20621430.18563436X-RAY DIFFRACTION100
3.44-4.340.1841460.15583464X-RAY DIFFRACTION100
4.34-48.250.17611520.18793571X-RAY DIFFRACTION99

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