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- PDB-5daq: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex... -

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Basic information

Entry
Database: PDB / ID: 5daq
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with 4-Methoxycyclopeptin
ComponentsPhytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230)
KeywordsOXIDOREDUCTASE / Antibiotics / Biosynthesis / Alkaloids / Viridicatin / Desaturase / Epoxidase / Fragmentation / 4-Methoxycyclopeptine
Function / homology
Function and homology information


(-)-cyclopenine synthase / dioxygenase activity / biosynthetic process / 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
Chem-58D / 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: 1.7 Å
AuthorsGroll, M. / Braeuer, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Structure of the Dioxygenase AsqJ: Mechanistic Insights into a One-Pot Multistep Quinolone Antibiotic Biosynthesis.
Authors: Brauer, A. / Beck, P. / Hintermann, L. / Groll, M.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Phytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4944
Polymers33,9791
Non-polymers5153
Water5,891327
1
A: Phytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230)
hetero molecules

A: Phytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9888
Polymers67,9582
Non-polymers1,0306
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area6890 Å2
ΔGint-55 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.730, 120.010, 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-664-

HOH

21A-688-

HOH

31A-729-

HOH

41A-780-

HOH

51A-794-

HOH

61A-806-

HOH

71A-822-

HOH

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Components

#1: Protein Phytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230) / AsqJ


Mass: 33978.855 Da / Num. of mol.: 1 / Fragment: UNP residues 110-416
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: AN9227.2, ANIA_09227 / Plasmid: pET28b(+) / Details (production host): Cleavable SUMO-fusion tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AR53
#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-58D / (3S)-3-(4-methoxybenzyl)-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione


Mass: 310.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 32625 / Num. obs: 32005 / % possible obs: 98.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.4
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAP

5dap


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.045 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19674 1601 5 %RANDOM
Rwork0.17519 ---
obs0.1764 30403 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.326 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å20 Å2
2--3.74 Å20 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 34 327 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192310
X-RAY DIFFRACTIONr_bond_other_d0.0020.022254
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9863152
X-RAY DIFFRACTIONr_angle_other_deg0.7993.0025188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7195287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81623.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23715385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9031516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212571
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
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_it1.2512.4051151
X-RAY DIFFRACTIONr_mcbond_other1.252.4011150
X-RAY DIFFRACTIONr_mcangle_it1.5393.5981437
X-RAY DIFFRACTIONr_mcangle_other1.543.6041438
X-RAY DIFFRACTIONr_scbond_it1.3022.6891159
X-RAY DIFFRACTIONr_scbond_other1.3012.6881160
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4323.9161716
X-RAY DIFFRACTIONr_long_range_B_refined2.920.5962813
X-RAY DIFFRACTIONr_long_range_B_other2.39819.7642660
X-RAY DIFFRACTIONr_rigid_bond_restr1.60434563
X-RAY DIFFRACTIONr_sphericity_free26.27594
X-RAY DIFFRACTIONr_sphericity_bonded4.93154748
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 116 -
Rwork0.359 2203 -
obs--99.02 %
Refinement TLS params.Method: refined / Origin x: -20.7126 Å / Origin y: -18.1322 Å / Origin z: -12.9993 Å
111213212223313233
T0.0153 Å20.0021 Å2-0.0015 Å2-0.0096 Å2-0.0002 Å2--0.0168 Å2
L0.6089 °20.103 °20.1916 °2-0.1712 °2-0.0011 °2--0.1132 °2
S-0.0235 Å °0.0198 Å °0.0298 Å °-0 Å °0.0171 Å °-0.038 Å °0.0014 Å °-0.0064 Å °0.0064 Å °

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