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- PDB-7e6w: Crystal structure of Sesquisabinene B Synthase 1 mutant G418A and... -

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Basic information

Entry
Database: PDB / ID: 7e6w
TitleCrystal structure of Sesquisabinene B Synthase 1 mutant G418A and F419N
ComponentsSesquisabinene B synthase 1
KeywordsLYASE / Terpene synthase / Santalum album / Farnesyl Pyrophosphate / sandalwood oil
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 synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Sesquisabinene B synthase 1
Similarity search - Component
Biological speciesSantalum album (white sandalwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSingh, S. / Thulasiram, H.V. / Kulkarni, K.A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP029426 India
CitationJournal: To Be Published
Title: Crystal structure of Sesquisabinene B Synthase 1 mutant G418A and F419N
Authors: Singh, S. / Thulasiram, H.V. / Kulkarni, K.A.
History
DepositionFeb 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sesquisabinene B synthase 1
B: Sesquisabinene B synthase 1


Theoretical massNumber of molelcules
Total (without water)128,4972
Polymers128,4972
Non-polymers00
Water00
1
A: Sesquisabinene B synthase 1


Theoretical massNumber of molelcules
Total (without water)64,2491
Polymers64,2491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sesquisabinene B synthase 1


Theoretical massNumber of molelcules
Total (without water)64,2491
Polymers64,2491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.067, 61.030, 182.710
Angle α, β, γ (deg.)90.00, 93.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sesquisabinene B synthase 1


Mass: 64248.648 Da / Num. of mol.: 2 / Mutation: G418A, F419N
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

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES (pH-6.5), 0.1M Magnesium Acetate, 10% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.1→47.58 Å / Num. obs: 21943 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 86.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.053 / Rrim(I) all: 0.097 / Net I/σ(I): 11.5
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3923 / CC1/2: 0.895 / Rpim(I) all: 0.554 / Rrim(I) all: 1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSFeb 1,2021data reduction
Aimless1.11.21data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K16

6k16


Resolution: 3.1→45.61 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 34.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 1074 4.96 %
Rwork0.2379 --
obs0.2398 21671 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8165 0 0 0 8165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118362
X-RAY DIFFRACTIONf_angle_d1.55311342
X-RAY DIFFRACTIONf_dihedral_angle_d19.8153036
X-RAY DIFFRACTIONf_chiral_restr0.0921249
X-RAY DIFFRACTIONf_plane_restr0.011441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.39271360.35652567X-RAY DIFFRACTION99
3.24-3.410.33381430.32232552X-RAY DIFFRACTION98
3.41-3.630.35871400.26622534X-RAY DIFFRACTION99
3.63-3.910.27051170.25662548X-RAY DIFFRACTION98
3.91-4.30.26351390.2332564X-RAY DIFFRACTION99
4.3-4.920.29821200.21432601X-RAY DIFFRACTION99
4.92-6.20.31371170.24782624X-RAY DIFFRACTION99
6.2-45.610.21141620.19712607X-RAY DIFFRACTION97
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)
12.5391-0.6841-2.23231.77161.923211.4290.08130.33030.0976-0.0053-0.17240.26870.0677-1.51560.02250.445-0.0615-0.2180.58940.06190.719610.751614.282469.8944
22.25790.6259-1.33612.492-1.77497.46240.13570.21880.0624-0.3578-0.1058-0.2208-0.05780.3568-0.1020.63130.1225-0.14360.6348-0.07260.6223-15.893413.101121.4154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 36:563)
2X-RAY DIFFRACTION2(chain B and resseq 36:563)

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