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- PDB-9c7k: Crystal structure of pentalenene synthase variant F76A with PEG m... -

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Basic information

Entry
Database: PDB / ID: 9c7k
TitleCrystal structure of pentalenene synthase variant F76A with PEG molecule in the active site
ComponentsPentalenene synthase
KeywordsMETAL BINDING PROTEIN / Terpene synthase / Cyclase / Sesquiterpene synthase
Function / homologypentalenene synthase / pentalenene synthase activity / : / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / antibiotic biosynthetic process / metal ion binding / Pentalenene synthase
Function and homology information
Biological speciesStreptomyces exfoliatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)77,01011
Polymers75,9492
Non-polymers1,0619
Water2,180121
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5536
Polymers37,9741
Non-polymers5785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4575
Polymers37,9741
Non-polymers4824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.417, 182.417, 56.306
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.55 Å3/Da / Density % sol: 65.39 %
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: 2.5→20 Å / Num. obs: 37349 / % possible obs: 99.8 % / Redundancy: 20.6 % / Biso Wilson estimate: 60.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 21.4 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4171 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.98 Å / SU ML: 0.3218 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3067
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1861 4.99 %
Rwork0.2109 35470 -
obs0.2122 37331 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 61 121 4908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00144891
X-RAY DIFFRACTIONf_angle_d0.39386639
X-RAY DIFFRACTIONf_chiral_restr0.0342699
X-RAY DIFFRACTIONf_plane_restr0.0039878
X-RAY DIFFRACTIONf_dihedral_angle_d11.53111767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.31211530.28842693X-RAY DIFFRACTION99.96
2.57-2.640.28971690.27922681X-RAY DIFFRACTION99.96
2.64-2.730.32581520.27912690X-RAY DIFFRACTION100
2.73-2.830.33361400.26632705X-RAY DIFFRACTION99.93
2.83-2.940.30681530.26552717X-RAY DIFFRACTION100
2.94-3.070.27421330.25882700X-RAY DIFFRACTION99.96
3.07-3.230.29851640.26842701X-RAY DIFFRACTION100
3.23-3.440.26111370.24792710X-RAY DIFFRACTION100
3.44-3.70.2381470.21662723X-RAY DIFFRACTION99.93
3.7-4.070.20711220.18952775X-RAY DIFFRACTION99.97
4.07-4.650.19261230.18312761X-RAY DIFFRACTION100
4.65-5.840.2021450.19662742X-RAY DIFFRACTION100
5.84-19.980.21961230.17062872X-RAY DIFFRACTION99.97

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