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- PDB-9c7j: Crystal structure of caryolan-1-ol synthase complexed with 2-fluo... -

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Basic information

Entry
Database: PDB / ID: 9c7j
TitleCrystal structure of caryolan-1-ol synthase complexed with 2-fluorofarnesyl diphosphate
Components(+)-caryolan-1-ol synthase
KeywordsMETAL BINDING PROTEIN / Terpene synthase / Cyclase / Sesquiterpene synthase / Inhibitor / Complex
Function / homology
Function and homology information


(+)-caryolan-1-ol synthase / (+)-beta-caryophyllene synthase / sesquiterpene synthase activity / sesquiterpenoid biosynthetic process / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / 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
DIPHOSPHATE / Chem-FPF / PHOSPHATE ION / (+)-caryolan-1-ol synthase
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPrem Kumar, R. / Black, B.Y. / 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)161,19618
Polymers158,7784
Non-polymers2,41814
Water4,576254
1
A: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2144
Polymers39,6951
Non-polymers5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3644
Polymers39,6951
Non-polymers6693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3095
Polymers39,6951
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: (+)-caryolan-1-ol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3095
Polymers39,6951
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.648, 89.606, 114.814
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 268 molecules

#2: Chemical
ChemComp-FPF / (2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 400.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H27FO7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.11 %
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: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 13, 2020
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 40108 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.212 / Net I/σ(I): 8.2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5805 / CC1/2: 0.71 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.99 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1977 4.94 %
Rwork0.2043 --
obs0.2065 40003 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9428 0 142 254 9824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019769
X-RAY DIFFRACTIONf_angle_d0.38813264
X-RAY DIFFRACTIONf_dihedral_angle_d12.3773577
X-RAY DIFFRACTIONf_chiral_restr0.0331394
X-RAY DIFFRACTIONf_plane_restr0.0041763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.32781530.26792652X-RAY DIFFRACTION99
2.72-2.790.27821430.25122703X-RAY DIFFRACTION99
2.79-2.870.28261320.23572735X-RAY DIFFRACTION99
2.87-2.960.34731350.24642710X-RAY DIFFRACTION99
2.96-3.070.27571510.24392662X-RAY DIFFRACTION99
3.07-3.190.29361140.23172753X-RAY DIFFRACTION99
3.19-3.340.25661480.22452716X-RAY DIFFRACTION99
3.34-3.510.27921680.2122687X-RAY DIFFRACTION99
3.51-3.730.3161400.24352666X-RAY DIFFRACTION97
3.73-4.020.19571430.18092727X-RAY DIFFRACTION99
4.02-4.420.18211260.16992735X-RAY DIFFRACTION99
4.42-5.050.23571490.16722735X-RAY DIFFRACTION99
5.05-6.320.22551280.20212784X-RAY DIFFRACTION99
6.32-19.990.20521470.16512761X-RAY DIFFRACTION98

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