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- PDB-9d28: Crystal structure of (+)-sabinene synthase from Thuja plicata -

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Basic information

Entry
Database: PDB / ID: 9d28
TitleCrystal structure of (+)-sabinene synthase from Thuja plicata
ComponentsSabinene synthase
KeywordsLYASE / Biosynthesis / Terpene / Cyclization
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
Biological speciesThuja plicata (western redcedar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsGaynes, M.N. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2024
Title: Structure and Function of Sabinene Synthase, a Monoterpene Cyclase That Generates a Highly Strained [3.1.0] Bicyclic Product.
Authors: Gaynes, M.N. / Osika, K.R. / Christianson, D.W.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Dec 11, 2024Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sabinene synthase
A: Sabinene synthase
C: Sabinene synthase
D: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)256,4654
Polymers256,4654
Non-polymers00
Water3,513195
1
B: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sabinene synthase


Theoretical massNumber of molelcules
Total (without water)64,1161
Polymers64,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.290, 89.810, 194.520
Angle α, β, γ (deg.)90.000, 134.890, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Sabinene synthase


Mass: 64116.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thuja plicata (western redcedar) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9WS05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mg/ml sabinene synthase, 3.5 M sodium formate (pH 7.0), 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.32→96.81 Å / Num. obs: 143268 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 50.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Net I/σ(I): 13.4
Reflection shellResolution: 2.32→2.4 Å / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14298 / CC1/2: 0.811 / Rpim(I) all: 0.418

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→96.81 Å / SU ML: 0.3208 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 3875 1.38 %
Rwork0.2127 276878 -
obs0.213 143073 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.89 Å2
Refinement stepCycle: LAST / Resolution: 2.32→96.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16050 0 0 195 16245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007216400
X-RAY DIFFRACTIONf_angle_d0.900922317
X-RAY DIFFRACTIONf_chiral_restr0.04982479
X-RAY DIFFRACTIONf_plane_restr0.00692900
X-RAY DIFFRACTIONf_dihedral_angle_d14.35235836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.33681340.3519918X-RAY DIFFRACTION99.48
2.35-2.380.3841420.32729898X-RAY DIFFRACTION99.35
2.38-2.410.37471440.31179937X-RAY DIFFRACTION99.5
2.41-2.440.2921420.30579903X-RAY DIFFRACTION99.26
2.44-2.480.2891360.30039887X-RAY DIFFRACTION99.1
2.48-2.510.3181430.29499938X-RAY DIFFRACTION99.33
2.51-2.550.32731330.29129853X-RAY DIFFRACTION98.61
2.55-2.60.34211440.2819817X-RAY DIFFRACTION98.04
2.6-2.640.30181380.27799812X-RAY DIFFRACTION97.71
2.64-2.690.32621420.26249580X-RAY DIFFRACTION96.72
2.69-2.740.27221360.27399986X-RAY DIFFRACTION99.39
2.74-2.80.33611480.26429907X-RAY DIFFRACTION99.49
2.8-2.860.31521360.25759887X-RAY DIFFRACTION99.41
2.86-2.920.26431370.2589992X-RAY DIFFRACTION99.68
2.92-30.32271480.25979972X-RAY DIFFRACTION99.43
3-3.080.26181420.25619918X-RAY DIFFRACTION99.72
3.08-3.170.25131300.26359908X-RAY DIFFRACTION99.37
3.17-3.270.29071270.23239936X-RAY DIFFRACTION99.23
3.27-3.390.21381460.2329952X-RAY DIFFRACTION99.48
3.39-3.520.23851400.2119831X-RAY DIFFRACTION98.64
3.52-3.680.26991360.20199973X-RAY DIFFRACTION99.16
3.68-3.880.23621300.18699713X-RAY DIFFRACTION97.47
3.88-4.120.23061420.18519916X-RAY DIFFRACTION99.12
4.12-4.440.19071230.16169921X-RAY DIFFRACTION99.62
4.44-4.880.18421410.16919961X-RAY DIFFRACTION99.59
4.88-5.590.22771500.18889948X-RAY DIFFRACTION99.4
5.59-7.040.20261260.21269904X-RAY DIFFRACTION99.36
7.04-96.810.14721390.15489710X-RAY DIFFRACTION96.91

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