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- PDB-7olq: Dioxygenase AsqJ mutant (V72I) in complex with 2 and Tris -

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Basic information

Entry
Database: PDB / ID: 7olq
TitleDioxygenase AsqJ mutant (V72I) in complex with 2 and Tris
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 / BROMIDE ION / NICKEL (II) ION / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Function and homology information
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,7136
Polymers34,0641
Non-polymers6495
Water66737
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)69,42612
Polymers68,1282
Non-polymers1,29810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7440 Å2
ΔGint-51 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.320, 121.270, 66.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-536-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 34063.965 Da / Num. of mol.: 1 / Mutation: A72I
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

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Non-polymers , 5 types, 42 molecules

#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-58J / 4-Methoxydehydrocyclopeptin


Mass: 308.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 100 mM TRIS/HCl, 1.25 M LiBr, 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: 2.05→30 Å / Num. obs: 18795 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.2
Reflection shellResolution: 2.05→2.15 Å / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2491 / % possible all: 98.7

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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: 2.05→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 16.652 / SU ML: 0.181 / 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
Rfree0.2384 939 5 %RANDOM
Rwork0.2028 ---
obs0.2047 17849 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.85 Å2 / Biso mean: 40.506 Å2 / Biso min: 22.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å2-0 Å2
2--0.59 Å20 Å2
3----3.51 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 34 37 2290
Biso mean--43.36 41.87 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172193
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6543150
X-RAY DIFFRACTIONr_angle_other_deg1.0781.5755085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21821.682107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6521516
X-RAY DIFFRACTIONr_chiral_restr0.0420.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022542
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02451
X-RAY DIFFRACTIONr_rigid_bond_restr0.41634498
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 68 -
Rwork0.353 1295 -
all-1363 -
obs--98.41 %
Refinement TLS params.Method: refined / Origin x: -20.971 Å / Origin y: -18.268 Å / Origin z: -13.294 Å
111213212223313233
T0.0007 Å20.001 Å20.0023 Å2-0.0508 Å2-0.0014 Å2--0.0455 Å2
L0.0811 °2-0.0105 °20.0382 °2-0.0885 °2-0.0172 °2--0.0773 °2
S-0.0032 Å °0.0018 Å °0.0057 Å °-0.0008 Å °0.0048 Å °-0.0093 Å °0.0033 Å °0.0044 Å °-0.0016 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 295
2X-RAY DIFFRACTION1A401 - 403

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