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- PDB-6sbc: Structure of type II terpene cyclase MstE from Scytonema in compl... -

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Basic information

Entry
Database: PDB / ID: 6sbc
TitleStructure of type II terpene cyclase MstE from Scytonema in complex with farnesyl dihydroxybenzoate
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 / farnesyl dihydroxybenzoate / MstE
Function and homology information
Biological speciesScytonema sp. PCC 10023 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)41,1998
Polymers40,6521
Non-polymers5467
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-48 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.980, 77.420, 90.910
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: 40652.402 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-L4H / farnesyl dihydroxybenzoate


Mass: 358.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, 4 M NaCl

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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: Aug 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 72004 / % possible obs: 95.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 15.7
Reflection shellResolution: 1.35→1.45 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 14057

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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: 1.35→15 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.39 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.046
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1531 3598 5 %RANDOM
Rwork0.1154 ---
obs0.1173 68352 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.31 Å2 / Biso mean: 18.347 Å2 / Biso min: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å20 Å2
2---0.61 Å20 Å2
3----3.04 Å2
Refinement stepCycle: final / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 32 310 3100
Biso mean--25.73 35.15 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132899
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172558
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.6393973
X-RAY DIFFRACTIONr_angle_other_deg1.7831.585914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4922.323155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92615419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.011517
X-RAY DIFFRACTIONr_chiral_restr0.1160.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023346
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02660
X-RAY DIFFRACTIONr_rigid_bond_restr5.6135457
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 268 -
Rwork0.244 5079 -
all-5347 -
obs--97.72 %
Refinement TLS params.Method: refined / Origin x: 6.9338 Å / Origin y: -3.3327 Å / Origin z: -21.3532 Å
111213212223313233
T0.0001 Å2-0 Å20.0001 Å2-0.0124 Å20.0001 Å2--0.0165 Å2
L0.0109 °2-0.0006 °2-0.0023 °2-0.0081 °20.0028 °2--0.0061 °2
S0.0001 Å °0.0001 Å °-0.0003 Å °0.0008 Å °-0 Å °-0.0003 Å °0.0003 Å °0.0007 Å °-0.0001 Å °

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