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

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Basic information

Entry
Database: PDB / ID: 5dav
TitleFe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with 4-Methoxydehydrocyclopeptin
ComponentsPhytanoyl-CoA dioxygenase family protein (AFU_orthologue AFUA_8G00230)
KeywordsOXIDOREDUCTASE / Antibiotics / Biosynthesis / Alkaloids / Viridicatin / Desaturase / Epoxidase / Fragmentation / 4-Methoxydehydrocyclopeptin
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
4-Methoxydehydrocyclopeptin / BROMIDE ION / : / NICKEL (II) ION / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGroll, M. / Braeuer, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
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: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)34,6677
Polymers33,9791
Non-polymers6886
Water4,288238
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)69,33414
Polymers67,9582
Non-polymers1,37612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area8010 Å2
ΔGint-51 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.050, 120.770, 66.660
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-644-

HOH

21A-654-

HOH

31A-715-

HOH

41A-716-

HOH

51A-727-

HOH

61A-729-

HOH

71A-736-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.) Aspergillus nidulans FGSC A4 (mold) / Gene: AN9227.2, ANIA_09227 / Plasmid: pET28b(+) / Details (production host): Cleavable SUMO-fusion tag / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AR53

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Non-polymers , 6 types, 244 molecules

#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-58J / 4-Methoxydehydrocyclopeptin


Mass: 308.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.16 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: Jun 13, 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: 1.8→30 Å / Num. all: 27710 / Num. obs: 27599 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.0066 / Net I/σ(I): 18.6
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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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: 1.8→15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.886 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19618 1380 5 %RANDOM
Rwork0.1644 ---
obs0.16622 26218 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.146 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å2-0 Å20 Å2
2--2.8 Å20 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 35 238 2500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192308
X-RAY DIFFRACTIONr_bond_other_d0.0010.022258
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9853150
X-RAY DIFFRACTIONr_angle_other_deg0.74135194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36123.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96215385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0381516
X-RAY DIFFRACTIONr_chiral_restr0.0580.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212568
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02499
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_it1.0032.4791152
X-RAY DIFFRACTIONr_mcbond_other0.9992.4741150
X-RAY DIFFRACTIONr_mcangle_it1.343.7081437
X-RAY DIFFRACTIONr_mcangle_other1.3393.7131438
X-RAY DIFFRACTIONr_scbond_it1.1972.7091156
X-RAY DIFFRACTIONr_scbond_other1.1932.711156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3733.971714
X-RAY DIFFRACTIONr_long_range_B_refined2.40620.4812746
X-RAY DIFFRACTIONr_long_range_B_other2.16720.0772645
X-RAY DIFFRACTIONr_rigid_bond_restr0.86634566
X-RAY DIFFRACTIONr_sphericity_free25.019564
X-RAY DIFFRACTIONr_sphericity_bonded6.81954694
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 97 -
Rwork0.284 1858 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: -20.8692 Å / Origin y: -18.304 Å / Origin z: -13.0645 Å
111213212223313233
T0.0068 Å20.0018 Å20.0013 Å2-0.0019 Å20.0003 Å2--0.0075 Å2
L0.0676 °20.0173 °20.0136 °2-0.0212 °20.0108 °2--0.0119 °2
S-0.0051 Å °0.0022 Å °-0.0005 Å °0.0009 Å °0.0049 Å °-0.006 Å °-0.0006 Å °0.0018 Å °0.0002 Å °

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