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- PDB-6yq0: Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 durin... -

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Basic information

Entry
Database: PDB / ID: 6yq0
TitlePromiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis
ComponentsMonooxygenase
KeywordsANTIBIOTIC / lugdunomycin / keto-reduction / short chain alcohol reductase / Rossmann fold
Function / homology
Function and homology information


FAD binding / monooxygenase activity
Similarity search - Function
FAD-binding domain / FAD binding domain / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-P7K / Monooxygenase
Similarity search - Component
Biological speciesStreptomyces sp. QL37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsXiao, X. / Elsayed, S.S. / Wu, C. / van der Heul, H. / Prota, A. / Huang, J. / Guo, R. / Abrahams, J.P. / van Wezel, G.P.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Functional and Structural Insights into a Novel Promiscuous Ketoreductase of the Lugdunomycin Biosynthetic Pathway.
Authors: Xiao, X. / Elsayed, S.S. / Wu, C. / van der Heul, H.U. / Metsa-Ketela, M. / Du, C. / Prota, A.E. / Chen, C.C. / Liu, W. / Guo, R.T. / Abrahams, J.P. / van Wezel, G.P.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Monooxygenase
BBB: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,62320
Polymers53,5942
Non-polymers3,02818
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint22 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.104, 60.379, 88.221
Angle α, β, γ (deg.)90.000, 102.415, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein Monooxygenase /


Mass: 26797.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. QL37 (bacteria) / Gene: C5F59_12925
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2S6PN47
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-P7K / (3~{R})-8-methoxy-3-methyl-3-oxidanyl-2,4-dihydrobenzo[a]anthracene-1,7,12-trione


Mass: 336.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.1 M Na Malonate, 0.1 M BIS-TRIS prop, pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→49.495 Å / Num. obs: 431114 / % possible obs: 95.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 11.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.3
Reflection shellResolution: 1.08→1.108 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 68021 / CC1/2: 0.801 / Rrim(I) all: 0.532 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4osp

4osp


Resolution: 1.08→49.495 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.152 / WRfactor Rwork: 0.138 / SU B: 0.874 / SU ML: 0.02 / Average fsc free: 0.9442 / Average fsc work: 0.9468 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1701 9703 5.035 %
Rwork0.1554 183000 -
all0.156 --
obs-192703 99.78 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 10.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.139 Å2
2--0.482 Å20 Å2
3----0.156 Å2
Refinement stepCycle: LAST / Resolution: 1.08→49.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3745 0 202 552 4499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0134094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173851
X-RAY DIFFRACTIONr_angle_refined_deg2.2061.6535575
X-RAY DIFFRACTIONr_angle_other_deg1.6621.5738881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.06521.25208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.42915639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8281537
X-RAY DIFFRACTIONr_chiral_restr0.3260.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02847
X-RAY DIFFRACTIONr_nbd_refined0.2380.2885
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23828
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22086
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2390
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3140.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.231
X-RAY DIFFRACTIONr_nbd_other0.2550.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.233
X-RAY DIFFRACTIONr_mcbond_it1.0350.8012056
X-RAY DIFFRACTIONr_mcbond_other1.0240.7992054
X-RAY DIFFRACTIONr_mcangle_it1.5251.2072573
X-RAY DIFFRACTIONr_mcangle_other1.521.2072573
X-RAY DIFFRACTIONr_scbond_it2.0221.0262038
X-RAY DIFFRACTIONr_scbond_other2.0211.0272039
X-RAY DIFFRACTIONr_scangle_it2.9041.4662989
X-RAY DIFFRACTIONr_scangle_other2.9031.4662990
X-RAY DIFFRACTIONr_lrange_it3.84817.07318398
X-RAY DIFFRACTIONr_lrange_other3.68716.44317899
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.057808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.1080.2497250.24813494X-RAY DIFFRACTION99.9157
1.108-1.1380.2557250.25513145X-RAY DIFFRACTION99.9424
1.138-1.1710.1826950.18212797X-RAY DIFFRACTION99.9852
1.171-1.2070.1886860.17412418X-RAY DIFFRACTION99.9619
1.207-1.2470.2447070.23911896X-RAY DIFFRACTION99.5891
1.247-1.2910.1866180.17611657X-RAY DIFFRACTION99.7562
1.291-1.3390.2315340.20911324X-RAY DIFFRACTION99.53
1.339-1.3940.1596140.13910757X-RAY DIFFRACTION99.9912
1.394-1.4560.1535470.14410401X-RAY DIFFRACTION99.9726
1.456-1.5270.1625400.1449954X-RAY DIFFRACTION99.9048
1.527-1.610.1264680.1189495X-RAY DIFFRACTION100
1.61-1.7070.1394660.129000X-RAY DIFFRACTION99.9894
1.707-1.8250.1413980.1178442X-RAY DIFFRACTION99.9887
1.825-1.9710.1873910.1797771X-RAY DIFFRACTION98.2781
1.971-2.1590.1373820.1227229X-RAY DIFFRACTION99.9737
2.159-2.4140.183290.1666510X-RAY DIFFRACTION99.0729
2.414-2.7870.1493040.135774X-RAY DIFFRACTION99.7866
2.787-3.4110.152650.1324894X-RAY DIFFRACTION99.8645
3.411-4.8190.161730.1333863X-RAY DIFFRACTION99.9257
4.819-49.4950.1731340.1772127X-RAY DIFFRACTION99.4721
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1893-0.02960.02160.05910.00260.06290.00160.01610.00660.01070.00440.00680.0097-0.0099-0.0060.0036-0.0007-0.00040.00650.00270.0088-21.232-31.9087-6.5983
20.08860.05180.08260.05180.01640.1825-0.0046-0.02130.0089-0.0022-0.0033-0.002-0.0141-0.0290.00790.00660.00190.0020.0097-0.00580.0056-7.5569-25.53721.106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 1601
2X-RAY DIFFRACTION2ALLBBB2 - 901

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