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- PDB-5oa7: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutan... -

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Basic information

Entry
Database: PDB / ID: 5oa7
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with cyclopeptin (1b)
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 / biosynthetic process / dioxygenase activity / metal ion binding
Similarity search - Function
Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
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: 1.65 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 / pdbx_struct_special_symmetry / 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

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)34,4784
Polymers33,9931
Non-polymers4853
Water5,134285
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)68,9568
Polymers67,9862
Non-polymers9706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area6880 Å2
ΔGint-57 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.830, 119.900, 67.140
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-637-

HOH

21A-642-

HOH

31A-751-

HOH

41A-766-

HOH

51A-768-

HOH

61A-778-

HOH

71A-782-

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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


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


Mass: 280.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 42.95 %
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: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 35034 / % possible obs: 98 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.1
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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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: 1.65→15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 6.678 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17392 1749 5 %RANDOM
Rwork0.13873 ---
obs0.14062 33229 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å2-0 Å2-0 Å2
2--2.75 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 32 285 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192309
X-RAY DIFFRACTIONr_bond_other_d0.0020.022190
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9853150
X-RAY DIFFRACTIONr_angle_other_deg0.9163.0025082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96623.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23215386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8871516
X-RAY DIFFRACTIONr_chiral_restr0.070.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
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_it1.6492.9911151
X-RAY DIFFRACTIONr_mcbond_other1.6482.9871150
X-RAY DIFFRACTIONr_mcangle_it2.1194.481437
X-RAY DIFFRACTIONr_mcangle_other2.1194.4831438
X-RAY DIFFRACTIONr_scbond_it1.8213.3521158
X-RAY DIFFRACTIONr_scbond_other1.823.3511159
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0884.8771714
X-RAY DIFFRACTIONr_long_range_B_refined3.28437.3542572
X-RAY DIFFRACTIONr_long_range_B_other2.87836.6232516
X-RAY DIFFRACTIONr_rigid_bond_restr0.80934499
X-RAY DIFFRACTIONr_sphericity_free26.9375185
X-RAY DIFFRACTIONr_sphericity_bonded8.87254550
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 128 -
Rwork0.354 2434 -
obs--99.46 %
Refinement TLS params.Method: refined / Origin x: -20.7647 Å / Origin y: -18.1596 Å / Origin z: -12.9518 Å
111213212223313233
T0.0008 Å20.0003 Å20.0012 Å2-0.0644 Å2-0.0003 Å2--0.018 Å2
L0.2127 °20.0166 °20.0343 °2-0.0622 °20.0066 °2--0.0135 °2
S-0.0111 Å °0.0031 Å °0.009 Å °-0.0003 Å °0.0123 Å °-0.0095 Å °-0.0023 Å °0.0007 Å °-0.0012 Å °

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