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- PDB-9c7l: Crystal structure of pentalenene synthase variant F76A complexed ... -

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Basic information

Entry
Database: PDB / ID: 9c7l
TitleCrystal structure of pentalenene synthase variant F76A complexed with 2-fluorofarnesyl diphosphate
ComponentsPentalenene synthase
KeywordsMETAL BINDING PROTEIN / Terpene synthase / Cyclase / Sesquiterpene synthase / complex / Inhibitors / Fluoro analog
Function / homology
Function and homology information


pentalenene synthase / pentalenene synthase activity / antibiotic biosynthetic process / metal 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
Chem-FPF / Pentalenene synthase
Similarity search - Component
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPrem Kumar, R. / Ellenburg, W.H. / 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

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Assembly

Deposited unit
A: Pentalenene synthase
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4226
Polymers75,9492
Non-polymers4734
Water6,053336
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4485
Polymers37,9741
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)37,9741
Polymers37,9741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.521, 181.521, 55.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Pentalenene synthase / PS / Pentalenolactone biosynthesis protein A / Sesquiterpene cyclase / Sesquiterpene synthase


Mass: 37974.316 Da / Num. of mol.: 2 / Mutation: F76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Gene: penA / Production host: Escherichia coli (E. coli) / References: UniProt: Q55012, pentalenene synthase
#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.: 1 / Source method: obtained synthetically / Formula: C15H27FO7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, containing 2 M ammonium sulfate and 2% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 53642 / % possible obs: 99.9 % / Redundancy: 20.9 % / Biso Wilson estimate: 46.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.119 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 21.3 % / Rmerge(I) obs: 1.86 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4642 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.84 Å / SU ML: 0.2639 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2809
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213 2713 5.06 %
Rwork0.1845 50909 -
obs0.1859 53622 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4995 0 28 336 5359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235157
X-RAY DIFFRACTIONf_angle_d0.50077006
X-RAY DIFFRACTIONf_chiral_restr0.0356731
X-RAY DIFFRACTIONf_plane_restr0.0051937
X-RAY DIFFRACTIONf_dihedral_angle_d14.03871898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.30461480.26622681X-RAY DIFFRACTION99.96
2.24-2.280.32731250.25642641X-RAY DIFFRACTION100
2.28-2.330.30331310.24292692X-RAY DIFFRACTION99.96
2.33-2.380.27351470.22972620X-RAY DIFFRACTION100
2.38-2.440.2621690.22572661X-RAY DIFFRACTION100
2.44-2.50.27821390.21982644X-RAY DIFFRACTION99.96
2.5-2.560.29011380.21752664X-RAY DIFFRACTION100
2.56-2.640.26691760.21232643X-RAY DIFFRACTION100
2.64-2.720.22591120.2172679X-RAY DIFFRACTION100
2.72-2.820.23551340.20772680X-RAY DIFFRACTION100
2.82-2.930.22351420.19982688X-RAY DIFFRACTION99.96
2.93-3.070.27051320.20442659X-RAY DIFFRACTION100
3.07-3.230.24851690.19892662X-RAY DIFFRACTION99.96
3.23-3.430.2471340.19122690X-RAY DIFFRACTION100
3.43-3.690.20251430.16652682X-RAY DIFFRACTION99.96
3.69-4.060.17171350.16132694X-RAY DIFFRACTION100
4.06-4.640.15031450.15212724X-RAY DIFFRACTION100
4.64-5.820.2041560.17132694X-RAY DIFFRACTION100
5.82-19.840.18051380.1732811X-RAY DIFFRACTION99.9

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