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- PDB-6oh7: Crystal structure of (E)-biformene synthase LrdC from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 6oh7
TitleCrystal structure of (E)-biformene synthase LrdC from Streptomyces sp. strain K155 in complex with Mg
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: 2.19 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: 5A0K
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.title / _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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8598
Polymers37,2401
Non-polymers6197
Water2,594144
1
A: Labdane-related diterpene synthase
hetero molecules

A: Labdane-related diterpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,71816
Polymers74,4802
Non-polymers1,23814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area5790 Å2
ΔGint-27 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.050, 107.050, 89.241
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Labdane-related diterpene synthase


Mass: 37240.109 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5
Details: 0.16 M MAGNESIUM ACETATE TETRAHYDRATE, 0.08 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 16% (W/V) PEG 8000, 20% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→34.27 Å / Num. obs: 30779 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 44.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.2
Reflection shellResolution: 2.19→2.26 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2 / Num. unique obs: 2617 / CC1/2: 0.726 / % possible all: 100

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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: 2.19→32.616 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.2
RfactorNum. reflection% reflection
Rfree0.2612 1598 5.2 %
Rwork0.2343 --
obs0.2357 30749 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.9 Å2 / Biso mean: 50.9221 Å2 / Biso min: 24.7 Å2
Refinement stepCycle: final / Resolution: 2.19→32.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 40 144 2568
Biso mean--58.75 53.14 -
Num. residues----311
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1901-2.26070.29411490.285825972746
2.2607-2.34150.35341240.274426572781
2.3415-2.43520.29231450.263725902735
2.4352-2.5460.3011600.263626242784
2.546-2.68020.27611350.261826452780
2.6802-2.8480.31211490.262426222771
2.848-3.06780.30531290.260326482777
3.0678-3.37620.30771370.255226492786
3.3762-3.86410.24021680.217826632831
3.8641-4.86580.22571620.203926572819
4.8658-32.61970.23141400.220127992939

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