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- PDB-9c7i: Crystal structure of caryolan-1-ol synthase from S. griseus with ... -

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Basic information

Entry
Database: PDB / ID: 9c7i
TitleCrystal structure of caryolan-1-ol synthase from S. griseus with PEG molecule in the active site
Components(+)-caryolan-1-ol synthase
KeywordsMETAL BINDING PROTEIN / Terpene synthase / Cyclase / Sesquiterpene synthase
Function / homology
Function and homology information


(+)-caryolan-1-ol synthase / (+)-beta-caryophyllene synthase / sesquiterpene synthase activity / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / sesquiterpenoid biosynthetic process / sesquiterpene biosynthetic process / manganese ion binding / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
(+)-caryolan-1-ol synthase
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsPrem Kumar, R. / Matos, J.O. / Oprian, D.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2024
Title: Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction.
Authors: Kumar, R.P. / Matos, J.O. / Black, B.Y. / Ellenburg, W.H. / Chen, J. / Patterson, M. / Gehtman, J.A. / Theobald, D.L. / Krauss, I.J. / Oprian, D.D.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (+)-caryolan-1-ol synthase
B: (+)-caryolan-1-ol synthase
C: (+)-caryolan-1-ol synthase
D: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,88414
Polymers158,7784
Non-polymers1,10510
Water13,818767
1
A: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9293
Polymers39,6951
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0134
Polymers39,6951
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0134
Polymers39,6951
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9293
Polymers39,6951
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.522, 89.804, 114.110
Angle α, β, γ (deg.)90.00, 90.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
(+)-caryolan-1-ol synthase / (+)-beta-caryophyllene synthase


Mass: 39694.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: gcoA, SGR_2079 / Production host: Escherichia coli (E. coli)
References: UniProt: B1W019, (+)-caryolan-1-ol synthase, (+)-beta-caryophyllene synthase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 28% PEG400, 200 mM CaCl2 and 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 9, 2019
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.33→90 Å / Num. obs: 59306 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.204 / Net I/σ(I): 7.5
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8660 / CC1/2: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
SCALAdata scaling
xia2data reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→70.57 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 2861 4.83 %
Rwork0.2114 --
obs0.2135 59266 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→70.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9381 0 64 767 10212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019648
X-RAY DIFFRACTIONf_angle_d0.38513063
X-RAY DIFFRACTIONf_dihedral_angle_d15.9453561
X-RAY DIFFRACTIONf_chiral_restr0.0331383
X-RAY DIFFRACTIONf_plane_restr0.0041739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.370.32531480.27552820X-RAY DIFFRACTION100
2.37-2.410.32331570.26712781X-RAY DIFFRACTION100
2.41-2.460.35941320.25792840X-RAY DIFFRACTION100
2.46-2.510.30381630.25912768X-RAY DIFFRACTION100
2.51-2.560.27971450.25652821X-RAY DIFFRACTION100
2.56-2.620.3291430.24332796X-RAY DIFFRACTION100
2.62-2.690.29081580.2432789X-RAY DIFFRACTION100
2.69-2.760.29471580.23162784X-RAY DIFFRACTION100
2.76-2.840.30811360.23032816X-RAY DIFFRACTION100
2.84-2.940.26341200.23122805X-RAY DIFFRACTION100
2.94-3.040.25841280.22442841X-RAY DIFFRACTION100
3.04-3.160.28051240.21882848X-RAY DIFFRACTION100
3.16-3.310.26991540.21922798X-RAY DIFFRACTION100
3.31-3.480.24341380.21842824X-RAY DIFFRACTION100
3.48-3.70.25771440.18722800X-RAY DIFFRACTION100
3.7-3.980.2121550.17612820X-RAY DIFFRACTION100
3.98-4.380.20161400.16852833X-RAY DIFFRACTION100
4.39-5.020.23451280.1752852X-RAY DIFFRACTION100
5.02-6.320.22071480.20942869X-RAY DIFFRACTION100
6.32-70.570.20761420.19312900X-RAY DIFFRACTION100

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