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- PDB-6sbg: Structure of type II terpene cyclase MstE_R337A from Scytonema in... -

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Basic information

Entry
Database: PDB / ID: 6sbg
TitleStructure of type II terpene cyclase MstE_R337A from Scytonema in complex with geranylgeranyl dihydroxybenzoate (substrate)
ComponentsMstE
KeywordsBIOSYNTHETIC PROTEIN / Type II Terpene Cyclase / Marine Drugs / Merosterol / Alpha6-Alpha6 Barrel
Function / homologySqualene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / geranylgeranyl dihydroxybenzoate / MstE
Function and homology information
Biological speciesScytonema sp. PCC 10023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoosmann, P. / Ecker, F. / Leopold-Messer, S. / Cahn, J.K.B. / Groll, M. / Piel, J.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation205321_165695 Switzerland
Swiss National Science Foundation205320_185077 Switzerland
CitationJournal: Nat.Chem. / Year: 2020
Title: A monodomain class II terpene cyclase assembles complex isoprenoid scaffolds.
Authors: Moosmann, P. / Ecker, F. / Leopold-Messer, S. / Cahn, J.K.B. / Dieterich, C.L. / Groll, M. / Piel, J.
History
DepositionJul 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MstE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0853
Polymers40,5661
Non-polymers5192
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.970, 77.750, 91.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MstE


Mass: 40566.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scytonema sp. PCC 10023 (bacteria) / Gene: mstE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D1CM82
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-L4E / geranylgeranyl dihydroxybenzoate


Mass: 426.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M LiCl, 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15698 / % possible obs: 99.3 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1866 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SBB

6sbb


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.196 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.237
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 781 5 %RANDOM
Rwork0.185 ---
obs0.1872 14846 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 30.262 Å2 / Biso min: 18.81 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å2-0 Å20 Å2
2---2.62 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 37 91 2872
Biso mean--55.83 33.24 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132882
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172539
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.643945
X-RAY DIFFRACTIONr_angle_other_deg1.1281.5865865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.895356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84822.434152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14415409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9781516
X-RAY DIFFRACTIONr_chiral_restr0.0370.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02651
X-RAY DIFFRACTIONr_rigid_bond_restr0.18835421
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 56 -
Rwork0.229 1060 -
all-1116 -
obs--99.64 %

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