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

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Basic information

Entry
Database: PDB / ID: 7oll
TitleDioxygenase AsqJ mutant (V72I) in complex with 2b and Tris
ComponentsIron/alpha-ketoglutarate-dependent dioxygenase asqJ
KeywordsOXIDOREDUCTASE / Quinolone Biosynthesis / Molecular Engineering / Epoxidation / Catalytic Mechanism
Function / homology
Function and homology information


(-)-cyclopenine synthase / biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH)
Similarity search - Domain/homology
BROMIDE ION / Chem-CO0 / NICKEL (II) ION / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)34,6126
Polymers33,9931
Non-polymers6195
Water1,76598
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)69,22412
Polymers67,9862
Non-polymers1,23810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7450 Å2
ΔGint-49 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.500, 121.310, 66.410
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-532-

HOH

21A-543-

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: 33992.883 Da / Num. of mol.: 1 / Mutation: V72I
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, 103 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO0 / (3~{Z})-4-methyl-3-(phenylmethylidene)-1~{H}-1,4-benzodiazepine-2,5-dione


Mass: 278.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 0.1 M TRIS, 1.25 M LiBr, 28% 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: 1.9→30 Å / Num. obs: 23325 / % possible obs: 98.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3303 / % possible all: 99.4

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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: 1.9→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 7.831 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.492 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 1166 5 %RANDOM
Rwork0.1657 ---
obs0.1672 22150 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.83 Å2 / Biso mean: 36.994 Å2 / Biso min: 26.37 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å2-0 Å2-0 Å2
2--1.71 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 32 98 2349
Biso mean--39.58 40.52 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172181
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.6543137
X-RAY DIFFRACTIONr_angle_other_deg1.0981.5745057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18321.682107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26815382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2511516
X-RAY DIFFRACTIONr_chiral_restr0.0430.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022534
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02451
X-RAY DIFFRACTIONr_rigid_bond_restr0.37234479
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 85 -
Rwork0.294 1615 -
all-1700 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: -21.0734 Å / Origin y: -18.2853 Å / Origin z: -13.3065 Å
111213212223313233
T0.0091 Å2-0.0014 Å2-0.0028 Å2-0.0097 Å2-0.0014 Å2--0.0214 Å2
L0.4012 °2-0.0103 °20.1044 °2-0.4067 °2-0.0185 °2--0.1069 °2
S-0.0255 Å °0.0193 Å °0.0297 Å °0.0026 Å °0.0179 Å °-0.0887 Å °0.0137 Å °-0.0101 Å °0.0076 Å °

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