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- PDB-6k16: Crystal Structure of Sesquisabinene B Synthase 1 from Santalum album -

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Basic information

Entry
Database: PDB / ID: 6k16
TitleCrystal Structure of Sesquisabinene B Synthase 1 from Santalum album
ComponentsSesquisabinene B synthase 1
KeywordsLYASE / Terpene synthase / Santalum album / sandalwood oil / Farnesyl Pyrophosphate
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase ...Terpene cyclase-like 1, C-terminal domain / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sesquisabinene B synthase 1
Similarity search - Component
Biological speciesSantalum album (white sandalwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSingh, S. / Thulasiram, H.V. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial ResearchBSC0124 India
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants
Authors: Singh, S. / Thulasiram, H.V. / Sengupta, D. / Kulkarni, K.
History
DepositionMay 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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: Sesquisabinene B synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2443
Polymers64,1961
Non-polymers492
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.059, 85.821, 53.399
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-739-

HOH

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Components

#1: Protein Sesquisabinene B synthase 1


Mass: 64195.555 Da / Num. of mol.: 1 / Mutation: G185K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Santalum album (white sandalwood) / Plasmid: pOPINSS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0A0A0RDR2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Magnesium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 14, 2017
Details: Cylindrical and Toridal mirrors with 50nm Pt-coating
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.16 Å / Num. obs: 32042 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.586 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.063 / Rrim(I) all: 0.095 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / Num. unique obs: 2760 / CC1/2: 0.781 / Rpim(I) all: 0.52 / Rrim(I) all: 0.775 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSJun 1,2017data reduction
Aimless0.5.21data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N0F

3n0f


Resolution: 2.2→36.572 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 2890 9.03 %
Rwork0.1974 --
obs0.2002 32010 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→36.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 2 48 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214189
X-RAY DIFFRACTIONf_angle_d1.6265680
X-RAY DIFFRACTIONf_dihedral_angle_d14.3181521
X-RAY DIFFRACTIONf_chiral_restr0.152624
X-RAY DIFFRACTIONf_plane_restr0.006722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23610.3441360.30621386X-RAY DIFFRACTION100
2.2361-2.27460.34721350.28761354X-RAY DIFFRACTION100
2.2746-2.3160.31111440.27461394X-RAY DIFFRACTION100
2.316-2.36050.3371290.27311398X-RAY DIFFRACTION100
2.3605-2.40870.27821280.25211390X-RAY DIFFRACTION100
2.4087-2.46110.2821210.24991392X-RAY DIFFRACTION100
2.4611-2.51830.34361490.26781383X-RAY DIFFRACTION100
2.5183-2.58130.27911390.24041388X-RAY DIFFRACTION100
2.5813-2.6510.29141380.24431367X-RAY DIFFRACTION100
2.651-2.7290.23561380.22781372X-RAY DIFFRACTION100
2.729-2.81710.25141390.22451391X-RAY DIFFRACTION100
2.8171-2.91770.25651380.2091373X-RAY DIFFRACTION100
2.9177-3.03450.25651400.20891382X-RAY DIFFRACTION99
3.0345-3.17250.26561400.22021395X-RAY DIFFRACTION99
3.1725-3.33970.23951380.20941387X-RAY DIFFRACTION100
3.3397-3.54880.23591390.19041379X-RAY DIFFRACTION100
3.5488-3.82250.19451390.17211386X-RAY DIFFRACTION99
3.8225-4.20670.18441370.16091373X-RAY DIFFRACTION100
4.2067-4.81420.20711410.16221413X-RAY DIFFRACTION100
4.8142-6.06090.18231400.19051393X-RAY DIFFRACTION100
6.0609-36.5770.17611420.15571424X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -27.5632 Å / Origin y: -15.0276 Å / Origin z: 13.1112 Å
111213212223313233
T0.2696 Å2-0.0164 Å20.0024 Å2-0.2567 Å20.0503 Å2--0.3944 Å2
L2.8242 °21.3856 °21.5341 °2-2.247 °20.8031 °2--2.0812 °2
S-0.1594 Å °0.0815 Å °-0.003 Å °-0.2083 Å °0.1288 Å °0.3288 Å °0.0643 Å °-0.1515 Å °0.0271 Å °
Refinement TLS groupSelection details: all

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