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

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Basic information

Entry
Database: PDB / ID: 7olm
TitleDioxygenase AsqJ mutant (V72I) in complex with 2b-O-O 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 / BROMIDE ION / NICKEL (II) ION / Chem-VJQ / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Function and homology information
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)34,6016
Polymers33,9931
Non-polymers6095
Water3,513195
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)69,20312
Polymers67,9862
Non-polymers1,21710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7410 Å2
ΔGint-79 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.210, 121.060, 66.730
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-604-

HOH

21A-682-

HOH

31A-687-

HOH

41A-690-

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 , 6 types, 200 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-VJQ / 3-[(S)-dioxidanyl(phenyl)methyl]-4-methyl-2-oxidanyl-1H-1,4-benzodiazepin-5-one


Mass: 312.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N2O4 / 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.: 1 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM TRIS/HCl, 1 M LiBr, 26% PEG 4000 / PH range: 8.2

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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: 1.75→30 Å / Num. obs: 29723 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4354 / % possible all: 95.3

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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: 1.75→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.995 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1486 5 %RANDOM
Rwork0.1745 ---
obs0.1759 28229 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.89 Å2 / Biso mean: 26.878 Å2 / Biso min: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å2-0 Å2
2--1.07 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 34 198 2460
Biso mean--30.09 35.18 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132315
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172204
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.6543159
X-RAY DIFFRACTIONr_angle_other_deg1.0951.5745112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89221.682107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18615388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4221516
X-RAY DIFFRACTIONr_chiral_restr0.0430.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022548
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02453
X-RAY DIFFRACTIONr_rigid_bond_restr0.24834518
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 108 -
Rwork0.328 2047 -
all-2155 -
obs--97.82 %
Refinement TLS params.Method: refined / Origin x: -20.897 Å / Origin y: -18.319 Å / Origin z: -13.033 Å
111213212223313233
T0.0003 Å2-0.0012 Å20.0007 Å2-0.0235 Å20.0001 Å2--0.0081 Å2
L0.0488 °20.009 °20.0045 °2-0.0195 °2-0.0022 °2--0.062 °2
S0.0017 Å °-0.0031 Å °0.0012 Å °-0.0012 Å °-0.0005 Å °-0.0038 Å °-0.0008 Å °0.0022 Å °-0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 295
2X-RAY DIFFRACTION1A401 - 403

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