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- PDB-7olr: Dioxygenase AsqJ in complex with 2 and alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 7olr
TitleDioxygenase AsqJ in complex with 2 and alpha-ketoglutarate
ComponentsIron/alpha-ketoglutarate-dependent dioxygenase asqJ
KeywordsOXIDOREDUCTASE / Quinolone Biosynthesis / Molecular Engineering / Epoxidation / Catalytic Mechanism
Function / homology(-)-cyclopenine synthase / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / metal ion binding / 4-Methoxydehydrocyclopeptin / 2-OXOGLUTARIC ACID / NICKEL (II) ION / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Function and homology information
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAuman, D. / Mader, S.L. / Ecker, F. / Dorst, K. / Braeuer, A. / Widmalm, G. / Groll, M. / Kaila, V.R.I.
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ.
Authors: Auman, D. / Ecker, F. / Mader, S.L. / Dorst, K.M. / Brauer, A. / Widmalm, G. / Groll, M. / Kaila, V.R.I.
History
DepositionMay 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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: Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4924
Polymers33,9791
Non-polymers5133
Water45025
1
A: Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
hetero molecules

A: Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9848
Polymers67,9582
Non-polymers1,0266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area6880 Å2
ΔGint-59 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.310, 115.900, 66.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Iron/alpha-ketoglutarate-dependent dioxygenase asqJ / 4'-methoxyviridicatin/aspoquinolone biosynthesis cluster protein asqJ / Aspoquinolone biosynthesis protein J


Mass: 33978.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: asqJ, AN9227 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5AR53, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-58J / 4-Methoxydehydrocyclopeptin


Mass: 308.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 100 mM TRIS/HCl, 1 M LiCl, 27% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 16153 / % possible obs: 95.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2096 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAP

5dap


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 19.729 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.216 807 5 %RANDOM
Rwork0.1915 ---
obs0.1927 15338 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.09 Å2 / Biso mean: 50.101 Å2 / Biso min: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.72 Å2-0 Å2-0 Å2
2--10.02 Å20 Å2
3----5.3 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 34 25 2277
Biso mean--60.93 58.53 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132301
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172175
X-RAY DIFFRACTIONr_angle_refined_deg1.221.6573141
X-RAY DIFFRACTIONr_angle_other_deg1.0561.5745044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73721.574108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6771516
X-RAY DIFFRACTIONr_chiral_restr0.0380.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022547
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02450
X-RAY DIFFRACTIONr_rigid_bond_restr0.34834474
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 60 -
Rwork0.334 1150 -
all-1210 -
obs--96.96 %
Refinement TLS params.Method: refined / Origin x: -20.7019 Å / Origin y: -17.0879 Å / Origin z: -13.777 Å
111213212223313233
T0.0461 Å20.0018 Å20.0011 Å2-0.0008 Å2-0 Å2--0.0302 Å2
L0.0438 °2-0.0074 °20.0163 °2-0.0232 °2-0.016 °2--0.0156 °2
S0.0017 Å °0.0038 Å °0.0096 Å °0.0017 Å °0.0022 Å °-0.0002 Å °-0.0013 Å °-0.0001 Å °-0.0039 Å °

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