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- PDB-8zg0: Drimenyl diphosphate synthase SsDMS_F248A&D303E from Streptomyces... -

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Basic information

Entry
Database: PDB / ID: 8zg0
TitleDrimenyl diphosphate synthase SsDMS_F248A&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: 1.98 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)57,5431
Polymers57,5431
Non-polymers00
Water8,269459
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.390, 114.280, 180.930
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 / Mutation: F248A,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.: 459 / 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: 2.32 Å3/Da / Density meas: 47.1 Mg/m3 / Density % sol: 46.71 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.9 / 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 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→90.46 Å / Num. obs: 37556 / % possible obs: 99.8 % / Redundancy: 11.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.056 / Net I/σ(I): 18.9
Reflection shellResolution: 1.98→2.09 Å / Num. unique obs: 5430 / CC1/2: 0.988

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
iMOSFLM3.27data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XQ4

7xq4


Resolution: 1.98→30.6 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 2000 5.34 %
Rwork0.1764 --
obs0.1787 37471 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 0 459 3983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.932
X-RAY DIFFRACTIONf_dihedral_angle_d4.773525
X-RAY DIFFRACTIONf_chiral_restr0.05553
X-RAY DIFFRACTIONf_plane_restr0.011660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.20521410.16152503X-RAY DIFFRACTION100
2.03-2.080.24791410.15762505X-RAY DIFFRACTION100
2.08-2.150.21171420.16262521X-RAY DIFFRACTION100
2.15-2.210.2141400.17282483X-RAY DIFFRACTION100
2.21-2.290.24291410.19222502X-RAY DIFFRACTION99
2.29-2.390.23831420.17492518X-RAY DIFFRACTION100
2.39-2.490.22381430.18042521X-RAY DIFFRACTION100
2.49-2.630.22391420.18622524X-RAY DIFFRACTION100
2.63-2.790.20231420.192523X-RAY DIFFRACTION100
2.79-3.010.25791440.19422561X-RAY DIFFRACTION100
3.01-3.310.22591440.18772552X-RAY DIFFRACTION100
3.31-3.790.19791430.16372549X-RAY DIFFRACTION100
3.79-4.770.1751470.15362592X-RAY DIFFRACTION100
4.77-30.60.2471480.19222617X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -17.5786 Å / Origin y: -5.6857 Å / Origin z: -20.6197 Å
111213212223313233
T0.0905 Å20.028 Å2-0.0082 Å2-0.1139 Å2-0.0013 Å2--0.0996 Å2
L0.2077 °2-0.0174 °20.109 °2-1.0728 °20.5323 °2--1.2726 °2
S0.0294 Å °0.0212 Å °0.0338 Å °-0.0313 Å °-0.006 Å °0.0318 Å °-0.0518 Å °-0.0668 Å °-0.0257 Å °
Refinement TLS groupSelection details: all

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