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- PDB-6oh8: Crystal structure of (E)-biformene synthase LrdC from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 6oh8
TitleCrystal structure of (E)-biformene synthase LrdC from Streptomyces sp. strain K155 in the dimeric form
ComponentsLabdane-related diterpene synthase
KeywordsLYASE / Bioactive natural products / biformene / diterpene synthase / labdatriene
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / : / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Terpene synthase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsCenteno-Leija, S. / Serrano-Posada, H.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)CB-2016-01-285001 Mexico
Consejo Nacional de Ciencia y Tecnologia (CONACYT)INFR-2017-01-280608 Mexico
CitationJournal: J.Struct.Biol. / Year: 2019
Title: The structure of (E)-biformene synthase provides insights into the biosynthesis of bacterial bicyclic labdane-related diterpenoids.
Authors: Centeno-Leija, S. / Tapia-Cabrera, S. / Guzman-Trampe, S. / Esquivel, B. / Esturau-Escofet, N. / Tierrafria, V.H. / Rodriguez-Sanoja, R. / Zarate-Romero, A. / Stojanoff, V. / Rudino-Pinera, ...Authors: Centeno-Leija, S. / Tapia-Cabrera, S. / Guzman-Trampe, S. / Esquivel, B. / Esturau-Escofet, N. / Tierrafria, V.H. / Rodriguez-Sanoja, R. / Zarate-Romero, A. / Stojanoff, V. / Rudino-Pinera, E. / Sanchez, S. / Serrano-Posada, H.
History
DepositionApr 4, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionApr 17, 2019ID: 5A0I
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Labdane-related diterpene synthase
B: Labdane-related diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1038
Polymers74,4802
Non-polymers6236
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, DIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-6 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.960, 104.160, 66.530
Angle α, β, γ (deg.)90.000, 111.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 141 or resid 143 through 314))
21(chain B and (resid 10 through 141 or resid 143 through 314))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 10 through 141 or resid 143 through 314))AA10 - 14110 - 141
12ALAALAHISHIS(chain A and (resid 10 through 141 or resid 143 through 314))AA143 - 314143 - 314
21METMETALAALA(chain B and (resid 10 through 141 or resid 143 through 314))BB10 - 14110 - 141
22ALAALAHISHIS(chain B and (resid 10 through 141 or resid 143 through 314))BB143 - 314143 - 314

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Components

#1: Protein Labdane-related diterpene synthase


Mass: 37240.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: STREPTOMYCES SP. STRAIN K155 WAS ISOLATED FROM SOIL FROM VALLE DE CHALCO, STATE OF MEXICO BY UNAM
Source: (gene. exp.) Streptomyces sp. (bacteria) / Plasmid: PET-22B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: A0A158RFK9, EC: 4.2.3.193
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2014
RadiationMonochromator: SI-111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.17→52.08 Å / Num. obs: 32973 / % possible obs: 98.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 31.38 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.152 / Net I/σ(I): 12
Reflection shellResolution: 2.17→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.426 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2496 / CC1/2: 0.351 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOW RESOLUTION SAD STRUCTURE

Resolution: 2.17→52.08 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.2383 1553 4.75 %
Rwork0.1953 --
obs0.1974 32692 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.03 Å2 / Biso mean: 40.2859 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 2.17→52.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 41 290 5006
Biso mean--37 39.48 -
Num. residues----611
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2472X-RAY DIFFRACTION15.471TORSIONAL
12B2472X-RAY DIFFRACTION15.471TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.24010.33341270.2772374250184
2.2401-2.32010.32471120.27482676278891
2.3201-2.4130.29531540.24322870302499
2.413-2.52280.28881250.229929013026100
2.5228-2.65580.28711330.225428883021100
2.6558-2.82220.24741200.22472921304199
2.8222-3.04010.27731570.216328943051100
3.0401-3.3460.25871470.20829063053100
3.346-3.83010.21071530.17962868302199
3.8301-4.82490.20261490.158629103059100
4.8249-52.0950.1981760.157729313107100

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