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- PDB-9d2a: Crystal structure of (+)-sabinene synthase from Thuja plicata: co... -

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Basic information

Entry
Database: PDB / ID: 9d2a
TitleCrystal structure of (+)-sabinene synthase from Thuja plicata: condition 3
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
: / Sabinene synthase
Similarity search - Component
Biological speciesThuja plicata (giant arborvitae)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
C: Sabinene synthase
D: Sabinene synthase
A: Sabinene synthase
B: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,54222
Polymers256,4654
Non-polymers1,07618
Water7,260403
1
C: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3555
Polymers64,1161
Non-polymers2394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3555
Polymers64,1161
Non-polymers2394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3555
Polymers64,1161
Non-polymers2394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Sabinene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4767
Polymers64,1161
Non-polymers3606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)274.483, 90.769, 193.942
Angle α, β, γ (deg.)90.000, 134.790, 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 (giant arborvitae) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9WS05
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL sabinene synthase, 3.5 M sodium formate (pH 7.0), 10 mM TCEP, soaked in metal and ligand solution overnight

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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: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.21→34.412 Å / Num. obs: 141612 / % possible obs: 94.1 % / Redundancy: 4 % / Biso Wilson estimate: 42.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.039 / Net I/σ(I): 10.1
Reflection shellResolution: 2.21→2.355 Å / Rmerge(I) obs: 0.789 / Num. unique obs: 1910 / CC1/2: 0.708 / Rpim(I) all: 0.446

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→34.41 Å / SU ML: 0.2665 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.882
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 2000 1.41 %
Rwork0.198 139529 -
obs0.1984 141529 83.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.73 Å2
Refinement stepCycle: LAST / Resolution: 2.21→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16182 0 33 403 16618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007516549
X-RAY DIFFRACTIONf_angle_d0.903522476
X-RAY DIFFRACTIONf_chiral_restr0.04732482
X-RAY DIFFRACTIONf_plane_restr0.00732910
X-RAY DIFFRACTIONf_dihedral_angle_d15.0355970
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.260.3204120.2733823X-RAY DIFFRACTION6.92
2.27-2.330.2963510.28873537X-RAY DIFFRACTION29.84
2.33-2.390.3497930.2666841X-RAY DIFFRACTION57.77
2.39-2.470.3081430.26639906X-RAY DIFFRACTION83.44
2.47-2.560.2831610.258511699X-RAY DIFFRACTION98.57
2.56-2.660.29381630.244611731X-RAY DIFFRACTION98.55
2.66-2.780.28761750.253111779X-RAY DIFFRACTION99.06
2.78-2.930.26471690.24311781X-RAY DIFFRACTION98.85
2.93-3.110.25771660.246911823X-RAY DIFFRACTION99.43
3.11-3.350.30961760.228411847X-RAY DIFFRACTION99.12
3.35-3.690.20161700.187411824X-RAY DIFFRACTION99.4
3.69-4.220.20031720.157911917X-RAY DIFFRACTION99.42
4.22-5.320.17371720.153511950X-RAY DIFFRACTION99.26
5.32-34.410.18491770.173212071X-RAY DIFFRACTION98.89

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