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- PDB-6sbe: Structure of type II terpene cyclase MstE_D109N from Scytonema in... -

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Basic information

Entry
Database: PDB / ID: 6sbe
TitleStructure of type II terpene cyclase MstE_D109N 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 / DI(HYDROXYETHYL)ETHER / MstE
Function and homology information
Biological speciesScytonema sp. PCC 10023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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

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Assembly

Deposited unit
A: MstE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7379
Polymers40,6511
Non-polymers1,0858
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint4 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.770, 77.320, 91.170
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: 40651.418 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-L4E / geranylgeranyl dihydroxybenzoate


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


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaOAc, 1 M LiCl, 30% PEG 6000

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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: 1.4→50 Å / Num. obs: 66882 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.5 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 12366

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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: 1.4→15 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.809 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1379 3340 5 %RANDOM
Rwork0.1007 ---
obs0.1026 63472 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.56 Å2 / Biso mean: 17.427 Å2 / Biso min: 9.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---1.24 Å20 Å2
3---1.4 Å2
Refinement stepCycle: final / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 74 324 3156
Biso mean--31.37 34.88 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132988
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172639
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.6414086
X-RAY DIFFRACTIONr_angle_other_deg1.7121.5856107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2922.42157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76115424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0771517
X-RAY DIFFRACTIONr_chiral_restr0.1110.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023438
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02669
X-RAY DIFFRACTIONr_rigid_bond_restr3.51435627
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 242 -
Rwork0.194 4605 -
all-4847 -
obs--99.57 %

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