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- PDB-9d29: Crystal structure of (+)-sabinene synthase from Thuja plicata: co... -

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Basic information

Entry
Database: PDB / ID: 9d29
TitleCrystal structure of (+)-sabinene synthase from Thuja plicata: condition 2
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: 2.72 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)258,92730
Polymers256,4654
Non-polymers2,46226
Water1,802100
1
A: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5896
Polymers64,1161
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8739
Polymers64,1161
Non-polymers7578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8739
Polymers64,1161
Non-polymers7578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5936
Polymers64,1161
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)271.992, 88.416, 190.649
Angle α, β, γ (deg.)90.000, 134.250, 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 5 mg/mL sabinene synthase, 0.1 M bis-tris (pH 5.5), 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.72→29.13 Å / Num. obs: 86085 / % possible obs: 98.8 % / Redundancy: 4 % / Biso Wilson estimate: 61.45 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.07 / Net I/σ(I): 8.3
Reflection shellResolution: 2.72→2.82 Å / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8101 / CC1/2: 0.511 / Rpim(I) all: 0.534

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→29.13 Å / SU ML: 0.359 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 1995 2.33 %
Rwork0.1778 83751 -
obs0.1787 85745 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.82 Å2
Refinement stepCycle: LAST / Resolution: 2.72→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16125 0 139 100 16364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008116593
X-RAY DIFFRACTIONf_angle_d0.910822576
X-RAY DIFFRACTIONf_chiral_restr0.04842499
X-RAY DIFFRACTIONf_plane_restr0.00722907
X-RAY DIFFRACTIONf_dihedral_angle_d15.69975884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.790.35061260.30695214X-RAY DIFFRACTION86.02
2.79-2.870.27071450.24716004X-RAY DIFFRACTION99.61
2.87-2.950.28151380.22766004X-RAY DIFFRACTION99.59
2.95-3.050.28421430.22946053X-RAY DIFFRACTION99.69
3.05-3.160.29091370.22175972X-RAY DIFFRACTION99.69
3.16-3.280.25011580.20386058X-RAY DIFFRACTION99.7
3.28-3.430.26711390.19685980X-RAY DIFFRACTION99.69
3.43-3.610.24081420.18216034X-RAY DIFFRACTION99.69
3.61-3.840.2151450.15976056X-RAY DIFFRACTION99.73
3.84-4.130.20331470.16036062X-RAY DIFFRACTION99.66
4.13-4.550.19671460.14366030X-RAY DIFFRACTION99.32
4.55-5.20.1861390.15176048X-RAY DIFFRACTION99.21
5.2-6.540.20461480.20086091X-RAY DIFFRACTION99.35
6.54-29.130.1661420.15086145X-RAY DIFFRACTION98.23

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