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- PDB-8zwz: terpene synthases with from Paramuricea clavata -

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Basic information

Entry
Database: PDB / ID: 8zwz
Titleterpene synthases with from Paramuricea clavata
ComponentsDiterpene synthase
KeywordsBIOSYNTHETIC PROTEIN / terpene synthases / coral / complex / Mg / alpha helix
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesParamuricea clavata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMao, J.J. / Chen, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270039 China
CitationJournal: Sci Adv / Year: 2025
Title: Mining coral-derived terpene synthases and mechanistic studies of the coral biflorane synthase.
Authors: Chen, B. / Mao, J. / Xu, K. / Liu, L. / Lin, W. / Guo, Y.W. / Wu, R. / Wang, C. / Xu, B.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diterpene synthase


Theoretical massNumber of molelcules
Total (without water)47,6951
Polymers47,6951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.284, 85.284, 106.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Diterpene synthase


Mass: 47694.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramuricea clavata (invertebrata) / Gene: PACLA_8A045082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6S7HXL7
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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Tri-lithium citrate 20% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→73.86 Å / Num. obs: 5948 / % possible obs: 99.78 % / Redundancy: 17.7 % / CC1/2: 0.967 / CC star: 0.992 / Net I/σ(I): 2.3
Reflection shellResolution: 3.501→3.626 Å / Num. unique obs: 572 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→73.86 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 266 4.49 %
Rwork0.2597 --
obs0.2612 5925 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→73.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 0 3330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.69
X-RAY DIFFRACTIONf_dihedral_angle_d5.929445
X-RAY DIFFRACTIONf_chiral_restr0.043522
X-RAY DIFFRACTIONf_plane_restr0.005578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-4.410.33621300.28022773X-RAY DIFFRACTION100
4.41-73.860.2641360.24542886X-RAY DIFFRACTION100

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