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- PDB-8zg1: Drimenyl diphosphate synthase SsDMS_F248Y&D303E from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 8zg1
TitleDrimenyl diphosphate synthase SsDMS_F248Y&D303E from Streptomyces showdoensis (Apo)
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 / Drimenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces showdoensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 8, 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


Theoretical massNumber of molelcules
Total (without water)57,6351
Polymers57,6351
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.580, 114.080, 181.020
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: 57634.887 Da / Num. of mol.: 1 / Mutation: F248Y,D303E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces showdoensis (bacteria) / Gene: VO63_21045 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2P2GK84
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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 meas: 47.2 Mg/m3 / Density % sol: 46.76 %
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: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→90.51 Å / Num. obs: 20686 / % possible obs: 96.8 % / Redundancy: 6.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.7
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 2925 / CC1/2: 0.861

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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: 2.4→48.26 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1999 9.69 %
Rwork0.1939 --
obs0.1994 20630 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 0 146 3730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.523
X-RAY DIFFRACTIONf_dihedral_angle_d3.655534
X-RAY DIFFRACTIONf_chiral_restr0.035559
X-RAY DIFFRACTIONf_plane_restr0.006671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.30861370.22621271X-RAY DIFFRACTION95
2.46-2.530.25711390.21741301X-RAY DIFFRACTION96
2.53-2.60.29791390.21741296X-RAY DIFFRACTION95
2.6-2.680.31251360.22411269X-RAY DIFFRACTION95
2.68-2.780.33061410.23341306X-RAY DIFFRACTION95
2.78-2.890.31751390.23031302X-RAY DIFFRACTION95
2.89-3.020.29561380.22251284X-RAY DIFFRACTION94
3.02-3.180.28561400.21291302X-RAY DIFFRACTION95
3.18-3.380.27441410.20771314X-RAY DIFFRACTION96
3.38-3.640.23541450.18761348X-RAY DIFFRACTION97
3.64-4.010.20621480.15891376X-RAY DIFFRACTION99
4.01-4.590.20251480.15511383X-RAY DIFFRACTION99
4.59-5.780.24261510.18181410X-RAY DIFFRACTION100
5.78-48.260.19471570.18291469X-RAY DIFFRACTION99

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