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- PDB-6xjj: Structure of non-heme iron enzyme TropC: Radical tropolone biosyn... -

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Basic information

Entry
Database: PDB / ID: 6xjj
TitleStructure of non-heme iron enzyme TropC: Radical tropolone biosynthesis
Components2-oxoglutarate-dependent dioxygenase tropC
KeywordsOXIDOREDUCTASE / Tropolone
Function / homology
Function and homology information


small molecule biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / dioxygenase activity / metal ion binding
Similarity search - Function
: / Non-haem dioxygenase N-terminal domain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
ACETATE ION / : / YTTRIUM (III) ION / 2-oxoglutarate-dependent dioxygenase tropC
Similarity search - Component
Biological speciesTalaromyces stipitatus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMallik, L. / Doyon, T.J. / Narayan, A.R.H. / Koutmos, M.
CitationJournal: Chemrxiv / Year: 2020
Title: Radical Tropolone Biosynthesis
Authors: Doyon, T.J. / Skinner, K. / Yang, D. / Mallik, L. / Wymore, T. / Koutmos, M. / Zimmerman, P.M. / Narayan, A.
History
DepositionJun 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-oxoglutarate-dependent dioxygenase tropC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2674
Polymers40,0641
Non-polymers2043
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.014, 111.014, 89.889
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 2-oxoglutarate-dependent dioxygenase tropC / Tropolone synthesis protein C


Mass: 40063.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (fungus)
Strain: ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006 / Gene: tropC, tsR5, TSTA_117800 / Production host: Escherichia coli (E. coli)
References: UniProt: B8M9K5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M Magnesium acetate, 20% PEG 8000, 0.01 M Yttrium (III) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 17, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→48.07 Å / Num. obs: 17040 / % possible obs: 95.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 64.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Χ2: 1.01 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.873 Å / Redundancy: 6 % / Rmerge(I) obs: 1.073 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2288 / CC1/2: 0.766 / Rpim(I) all: 0.72 / Rrim(I) all: 0.035 / Χ2: 1.04 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3Q

5c3q


Resolution: 2.7→48.07 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 796 4.68 %0.25
Rwork0.2103 ---
obs0.2122 17015 94.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 6 5 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052375
X-RAY DIFFRACTIONf_angle_d0.893221
X-RAY DIFFRACTIONf_dihedral_angle_d9.9411947
X-RAY DIFFRACTIONf_chiral_restr0.055345
X-RAY DIFFRACTIONf_plane_restr0.008419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.86920.3741410.34962717X-RAY DIFFRACTION97
2.8692-3.09070.30871350.28882638X-RAY DIFFRACTION94
3.0907-3.40160.30831020.25282551X-RAY DIFFRACTION90
3.4016-3.89350.26991210.21752783X-RAY DIFFRACTION98
3.8935-4.90420.23821590.18152766X-RAY DIFFRACTION97
4.9042-42.390.21451380.18422764X-RAY DIFFRACTION93

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