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- PDB-7zrn: Crystal structure of 10-epi-cubebol synthase from Sorangium cellu... -

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Basic information

Entry
Database: PDB / ID: 7zrn
TitleCrystal structure of 10-epi-cubebol synthase from Sorangium cellulosum (ScCubS) in complex with Pyrophosphate
Components10-epi-cubebol synthase
KeywordsPLANT PROTEIN / Lyase
Function / homology
Function and homology information


10-epi-cubebol synthase / lyase activity / metal ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
ACETATE ION / PYROPHOSPHATE / 10-epi-cubebol synthase
Similarity search - Component
Biological speciesSorangium cellulosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000354/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M017702/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L027593/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/S01778X/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2022
Title: How a 10- epi-Cubebol Synthase Avoids Premature Reaction Quenching to Form a Tricyclic Product at High Purity.
Authors: Whitehead, J.N. / Leferink, N.G.H. / Komati Reddy, G. / Levy, C.W. / Hay, S. / Takano, E. / Scrutton, N.S.
History
DepositionMay 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 10-epi-cubebol synthase
B: 10-epi-cubebol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,61211
Polymers79,0512
Non-polymers5619
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-75 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.315, 89.644, 100.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 10-epi-cubebol synthase


Mass: 39525.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum (bacteria) / Strain: So ce56 / Gene: sce6369 / Production host: Escherichia coli (E. coli) / References: UniProt: A9GK58, 10-epi-cubebol synthase
#2: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Imidazole, MES monohydrate acid pH 6.5, 0.03 M of each divalent cation, and 30% precipitant mix 2 40% v/v Ethylene glycol; 20% w/v PEG 8000
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.82→66.92 Å / Num. obs: 60876 / % possible obs: 99.92 % / Redundancy: 6.2 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1151 / Rpim(I) all: 0.0499 / Rrim(I) all: 0.1257 / Net I/σ(I): 9.36
Reflection shellResolution: 1.82→1.885 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.384 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 5964 / CC1/2: 0.506 / Rpim(I) all: 0.6683 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 1.82→66.92 Å / SU ML: 0.2006 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 2000 3.29 %
Rwork0.1748 58839 -
obs0.1758 60839 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.53 Å2
Refinement stepCycle: LAST / Resolution: 1.82→66.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4890 0 28 442 5360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00455176
X-RAY DIFFRACTIONf_angle_d0.77897072
X-RAY DIFFRACTIONf_chiral_restr0.0398743
X-RAY DIFFRACTIONf_plane_restr0.0123935
X-RAY DIFFRACTIONf_dihedral_angle_d10.2682709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.33151400.2894145X-RAY DIFFRACTION99.7
1.87-1.920.31381410.26844109X-RAY DIFFRACTION99.84
1.92-1.970.27541410.24334165X-RAY DIFFRACTION99.81
1.97-2.040.26741410.22464148X-RAY DIFFRACTION99.86
2.04-2.110.22781420.1924165X-RAY DIFFRACTION99.95
2.11-2.190.23541420.17294173X-RAY DIFFRACTION99.98
2.19-2.290.17971400.164159X-RAY DIFFRACTION100
2.29-2.410.22441430.16284191X-RAY DIFFRACTION99.93
2.41-2.570.1761430.16354195X-RAY DIFFRACTION100
2.57-2.760.19771430.16194191X-RAY DIFFRACTION100
2.76-3.040.21511430.16914210X-RAY DIFFRACTION100
3.04-3.480.1961440.16814255X-RAY DIFFRACTION100
3.48-4.390.17261450.15044277X-RAY DIFFRACTION100
4.39-66.920.18581520.1734456X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 73.9331860457 Å / Origin y: -5.20454116231 Å / Origin z: 0.00161027478401 Å
111213212223313233
T0.165707143993 Å2-0.00289712514383 Å20.00782654065021 Å2-0.17492138602 Å20.0195891582649 Å2--0.230257245502 Å2
L0.605705604959 °2-0.111607548299 °2-0.0201936703621 °2-0.370404372414 °20.28335844493 °2--0.859517102694 °2
S0.0043302311881 Å °-0.0196386298309 Å °0.0250854636132 Å °-0.0119538326684 Å °0.00580207909516 Å °-0.00843530859115 Å °-0.0136627807145 Å °0.0158219297346 Å °-0.00823745348018 Å °
Refinement TLS groupSelection details: all

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