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- PDB-9lpb: Terpene cyclase AriE mutant-D128A -

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Basic information

Entry
Database: PDB / ID: 9lpb
TitleTerpene cyclase AriE mutant-D128A
ComponentsTerpene synthase
KeywordsMETAL BINDING PROTEIN / cis-Eunicellane Cyclase
Function / homology: / Lyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene synthase
Function and homology information
Biological speciesAmycolatopsis arida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLi, F.R. / Yang, Q. / He, J.Y. / Sun, X.R. / Pan, X.M. / Xu, H.M. / Rudolf, J.D. / Dong, L.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82073746 China
CitationJournal: Chemistry / Year: 2025
Title: Crystal Structure and Catalytic Mechanism of the cis-Eunicellane Cyclase AriE.
Authors: Li, F.R. / Yang, Q. / He, J. / Sun, X. / Pan, X. / Xu, H.M. / Rudolf, J.D. / Dong, L.B.
History
DepositionJan 24, 2025Deposition site: PDBJ / Processing site: PDBC
SupersessionMay 7, 2025ID: 8ITQ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)42,4591
Polymers42,4591
Non-polymers00
Water4,197233
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)83.815, 83.815, 163.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

21A-466-

HOH

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Components

#1: Protein Terpene synthase


Mass: 42459.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis arida (bacteria) / Gene: SAMN05421810_102118 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I5P1T3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M potassium sodium tartrate, 100 mM imidazole, and 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.87→74.6 Å / Num. obs: 43669 / % possible obs: 88.3 % / Redundancy: 24.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.102 / Χ2: 0.83 / Net I/σ(I): 19.2 / Num. measured all: 1052358
Reflection shellResolution: 1.87→1.97 Å / % possible obs: 79.3 % / Redundancy: 17.7 % / Rmerge(I) obs: 0.954 / Num. measured all: 99076 / Num. unique obs: 5591 / CC1/2: 0.934 / Rpim(I) all: 0.228 / Rrim(I) all: 0.982 / Χ2: 0.62 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→29.63 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 1910 4.58 %
Rwork0.1788 --
obs0.18 41728 84.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 0 233 3096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.033
X-RAY DIFFRACTIONf_dihedral_angle_d14.7361075
X-RAY DIFFRACTIONf_chiral_restr0.061423
X-RAY DIFFRACTIONf_plane_restr0.027518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.910.27731110.27132185X-RAY DIFFRACTION79
1.93-1.960.23631040.2342133X-RAY DIFFRACTION86
1.96-2.020.24621450.20863000X-RAY DIFFRACTION91
2.02-2.090.2058920.21322053X-RAY DIFFRACTION62
2.09-2.160.20761460.18353146X-RAY DIFFRACTION95
2.16-2.20.1959700.19411456X-RAY DIFFRACTION96
2.27-2.350.22571180.19992500X-RAY DIFFRACTION97
2.35-2.470.23731590.1923286X-RAY DIFFRACTION98
2.47-2.630.22881590.20453297X-RAY DIFFRACTION99
2.63-2.830.23321590.19643325X-RAY DIFFRACTION99
2.83-3.120.21951620.18993368X-RAY DIFFRACTION100
3.12-3.570.22521540.1783208X-RAY DIFFRACTION95
3.57-4.490.18091560.15243235X-RAY DIFFRACTION94
4.49-29.630.17081750.1643626X-RAY DIFFRACTION100

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