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- PDB-6sbb: Structure of type II terpene cyclase MstE from Scytonema (apo) -

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Basic information

Entry
Database: PDB / ID: 6sbb
TitleStructure of type II terpene cyclase MstE from Scytonema (apo)
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 / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / MstE
Function and homology information
Biological speciesScytonema sp. PCC 10023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
B: MstE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6955
Polymers81,3052
Non-polymers3903
Water3,783210
1
A: MstE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0434
Polymers40,6521
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MstE


Theoretical massNumber of molelcules
Total (without water)40,6521
Polymers40,6521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.460, 48.580, 77.990
Angle α, β, γ (deg.)89.040, 99.970, 101.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MstE


Mass: 40652.402 Da / Num. of mol.: 2
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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM TRIS, 25% PEG 8000

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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: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 46089 / % possible obs: 92.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.4
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2 / Num. unique obs: 5260 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2SQC

2sqc


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 12.308 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 2304 5 %RANDOM
Rwork0.173 ---
obs0.1749 43775 92.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.56 Å2 / Biso mean: 43.701 Å2 / Biso min: 21.37 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20.16 Å21.42 Å2
2---2.39 Å20.51 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5372 0 26 210 5608
Biso mean--59.41 50 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195561
X-RAY DIFFRACTIONr_bond_other_d0.0010.024911
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9167591
X-RAY DIFFRACTIONr_angle_other_deg0.893311334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04523.745267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53415794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661534
X-RAY DIFFRACTIONr_chiral_restr0.0570.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021233
X-RAY DIFFRACTIONr_rigid_bond_restr0.509310472
X-RAY DIFFRACTIONr_sphericity_free29.895128
X-RAY DIFFRACTIONr_sphericity_bonded9.272510403
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 169 -
Rwork0.347 3218 -
all-3387 -
obs--92.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06420.03970.00030.0371-0.00710.08970.0060.00430.00330.0106-0.0071-0.00020.0033-0.00380.00110.0157-0.00150.0140.00690.00450.01898.6778-16.16728.0369
20.04020.0241-0.02250.06360.02240.11320.00130.0032-0.00330.0030.00060.0065-0.00630.0051-0.00180.0091-0.00140.01140.01380.00320.0182.945-21.5717-13.0275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 366
2X-RAY DIFFRACTION2B18 - 366

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