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- PDB-7ofl: Crystal structure of the sesquiterpene synthase Copu9 from coniop... -

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Basic information

Entry
Database: PDB / ID: 7ofl
TitleCrystal structure of the sesquiterpene synthase Copu9 from coniophora puteana in complex with alendronate
ComponentsTerpene synthase
KeywordsLYASE / terpene synthase / SESQUITERPENE / CYCLASE / TERPENOID
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / Terpene synthase
Function and homology information
Biological speciesConiophora puteana
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsDimos, N. / Loll, B.
CitationJournal: Microb Cell Fact / Year: 2022
Title: Biotechnological potential and initial characterization of two novel sesquiterpene synthases from Basidiomycota Coniophora puteana for heterologous production of delta-cadinol.
Authors: Ringel, M. / Dimos, N. / Himpich, S. / Haack, M. / Huber, C. / Eisenreich, W. / Schenk, G. / Loll, B. / Bruck, T.
History
DepositionMay 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,11924
Polymers85,6152
Non-polymers1,50522
Water12,556697
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-25 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.455, 76.622, 135.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-879-

HOH

21B-726-

HOH

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Components

#1: Protein Terpene synthase / Copu9


Mass: 42807.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coniophora puteana (strain RWD-64-598) (fungus)
Strain: RWD-64-598 / Gene: CONPUDRAFT_118913 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A5M3MXY8, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-AHD / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / ALENDRONATE / FOSAMAX (TM)


Mass: 245.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO7P2 / Comment: medication*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Magnesium formate 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 68244 / % possible obs: 98.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 35.7 Å2 / CC1/2: 0.989 / Rrim(I) all: 0.525 / Net I/σ(I): 8.73
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 10301 / CC1/2: 0.44 / Rrim(I) all: 3.02 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TJZ

6tjz


Resolution: 1.83→38.31 Å / SU ML: 0.2621 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2312 2082 3.08 %
Rwork0.1833 65589 -
obs0.1848 67671 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 90 697 6119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01315684
X-RAY DIFFRACTIONf_angle_d1.1547714
X-RAY DIFFRACTIONf_chiral_restr0.0628808
X-RAY DIFFRACTIONf_plane_restr0.01181018
X-RAY DIFFRACTIONf_dihedral_angle_d14.40872088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.36461210.34923811X-RAY DIFFRACTION86.82
1.88-1.920.3651380.3034340X-RAY DIFFRACTION99.87
1.92-1.970.33471390.27144372X-RAY DIFFRACTION99.71
1.97-2.030.29031370.25054337X-RAY DIFFRACTION99.49
2.03-2.10.29951380.22934348X-RAY DIFFRACTION99.25
2.1-2.170.29141390.22374386X-RAY DIFFRACTION99.76
2.17-2.260.23971390.20154371X-RAY DIFFRACTION99.71
2.26-2.360.23551400.17874397X-RAY DIFFRACTION99.78
2.36-2.490.261390.17294377X-RAY DIFFRACTION99.65
2.49-2.640.22731390.17624389X-RAY DIFFRACTION99.71
2.64-2.850.24111400.18134411X-RAY DIFFRACTION99.54
2.85-3.130.24161410.18014438X-RAY DIFFRACTION99.89
3.14-3.590.20111420.17124474X-RAY DIFFRACTION99.78
3.59-4.520.1931420.14554475X-RAY DIFFRACTION99.18
4.52-38.310.18531480.15844663X-RAY DIFFRACTION99.03

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