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- PDB-5oa8: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutan... -

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Basic information

Entry
Database: PDB / ID: 5oa8
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with demethylated cyclopeptin (1d)
ComponentsIron/alpha-ketoglutarate-dependent dioxygenase asqJ
KeywordsOXIDOREDUCTASE / Antibiotics / Quinolone Biosynthesis / Molecular Engineering / Desaturase / Catalytic Mechanism / Mutagenesis / pi-stacking
Function / homology
Function and homology information


(-)-cyclopenine synthase / dioxygenase activity / metal ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
demethylated cyclopeptin / 2-OXOGLUTARIC ACID / NICKEL (II) ION / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGroll, M. / Braeuer, A. / Kaila, V.R.I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ.
Authors: Mader, S.L. / Brauer, A. / Groll, M. / Kaila, V.R.I.
History
DepositionJun 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)34,4644
Polymers33,9931
Non-polymers4713
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)68,9288
Polymers67,9862
Non-polymers9426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area6910 Å2
ΔGint-58 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.090, 120.060, 67.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-594-

HOH

21A-674-

HOH

31A-685-

HOH

41A-693-

HOH

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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: 33992.883 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 (E. coli)
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
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-58L / demethylated cyclopeptin


Mass: 266.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2016
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 29922 / % possible obs: 99.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.4
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2.6 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAP

5dap


Resolution: 1.75→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 5.994 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.103 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19349 1492 5 %RANDOM
Rwork0.15676 ---
obs0.16066 28366 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å2-0 Å2
2--0.84 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 31 195 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192320
X-RAY DIFFRACTIONr_bond_other_d0.0020.022208
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9863168
X-RAY DIFFRACTIONr_angle_other_deg0.9023.0025126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5523.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26715390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4592.9071155
X-RAY DIFFRACTIONr_mcbond_other1.4562.9031154
X-RAY DIFFRACTIONr_mcangle_it1.9654.3531443
X-RAY DIFFRACTIONr_mcangle_other1.9654.3571444
X-RAY DIFFRACTIONr_scbond_it1.5543.261165
X-RAY DIFFRACTIONr_scbond_other1.5543.261166
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8074.7511724
X-RAY DIFFRACTIONr_long_range_B_refined3.03635.3032516
X-RAY DIFFRACTIONr_long_range_B_other2.77934.9562486
X-RAY DIFFRACTIONr_rigid_bond_restr1.20534528
X-RAY DIFFRACTIONr_sphericity_free25.7525126
X-RAY DIFFRACTIONr_sphericity_bonded9.40354546
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 107 -
Rwork0.287 2050 -
obs--99.36 %
Refinement TLS params.Method: refined / Origin x: -20.8594 Å / Origin y: -18.1903 Å / Origin z: -13.0504 Å
111213212223313233
T0.0014 Å20.0002 Å20.0005 Å2-0.0698 Å2-0.0003 Å2--0.0191 Å2
L0.122 °20.0294 °20.039 °2-0.0382 °20.0054 °2--0.0131 °2
S-0.0095 Å °0.0018 Å °-0.0044 Å °0.0011 Å °0.0097 Å °-0.0152 Å °-0.0035 Å °-0.0032 Å °-0.0002 Å °

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