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

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Basic information

Entry
Database: PDB / ID: 6ypz
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 / Short-chain dehydrogenase/reductase SDR / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / DI(HYDROXYETHYL)ETHER / 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)56,04218
Polymers53,5942
Non-polymers2,44816
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint21 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.828, 59.965, 88.428
Angle α, β, γ (deg.)90.000, 102.513, 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(DE3) (bacteria) / References: UniProt: A0A2S6PN47
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291.15 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→49.3 Å / Num. obs: 428985 / % possible obs: 95.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 12.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.064 / Rsym value: 0.054 / Net I/σ(I): 13.4
Reflection shellResolution: 1.08→1.108 Å / Redundancy: 3 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 67732 / CC1/2: 0.648 / Rrim(I) all: 0.827 / Rsym value: 0.679 / % possible all: 99.1

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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→49.298 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.15 / WRfactor Rwork: 0.131 / SU B: 0.947 / SU ML: 0.021 / Average fsc free: 0.9365 / Average fsc work: 0.939 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1653 9588 5.009 %
Rwork0.1457 181839 -
all0.147 --
obs-191427 99.91 %
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: 11.858 Å2
Baniso -1Baniso -2Baniso -3
1--0.316 Å20 Å2-0.244 Å2
2--0.492 Å20 Å2
3----0.062 Å2
Refinement stepCycle: LAST / Resolution: 1.08→49.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 158 508 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0134028
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173818
X-RAY DIFFRACTIONr_angle_refined_deg2.2151.6545468
X-RAY DIFFRACTIONr_angle_other_deg1.6541.5748803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.61520.952210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.42215636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1151539
X-RAY DIFFRACTIONr_chiral_restr0.1270.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024577
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02842
X-RAY DIFFRACTIONr_nbd_refined0.2350.2885
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23795
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22040
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2372
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3180.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.232
X-RAY DIFFRACTIONr_nbd_other0.2850.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.236
X-RAY DIFFRACTIONr_mcbond_it1.1140.9042044
X-RAY DIFFRACTIONr_mcbond_other1.1010.9022042
X-RAY DIFFRACTIONr_mcangle_it1.6581.362557
X-RAY DIFFRACTIONr_mcangle_other1.6511.3592557
X-RAY DIFFRACTIONr_scbond_it2.1171.1411984
X-RAY DIFFRACTIONr_scbond_other2.1171.1421985
X-RAY DIFFRACTIONr_scangle_it3.0561.6222900
X-RAY DIFFRACTIONr_scangle_other3.0561.6232901
X-RAY DIFFRACTIONr_lrange_it4.23519.09518116
X-RAY DIFFRACTIONr_lrange_other4.05718.47617668
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.057811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.1080.2666690.2713457X-RAY DIFFRACTION99.9646
1.108-1.1380.2357300.23613024X-RAY DIFFRACTION99.9346
1.138-1.1710.2236770.21112678X-RAY DIFFRACTION99.9701
1.171-1.2070.2126680.20212363X-RAY DIFFRACTION99.9923
1.207-1.2470.1896460.18711921X-RAY DIFFRACTION99.9841
1.247-1.2910.1895960.17511593X-RAY DIFFRACTION99.9672
1.291-1.3390.175540.15811216X-RAY DIFFRACTION99.983
1.339-1.3940.1845390.15510821X-RAY DIFFRACTION99.9736
1.394-1.4560.1585540.14210280X-RAY DIFFRACTION100
1.456-1.5270.1645530.1369877X-RAY DIFFRACTION99.9808
1.527-1.610.1485090.1289364X-RAY DIFFRACTION99.9797
1.61-1.7070.1424580.1258896X-RAY DIFFRACTION100
1.707-1.8250.1384360.1218375X-RAY DIFFRACTION99.9886
1.825-1.9710.1493850.1257824X-RAY DIFFRACTION99.9878
1.971-2.1590.1423990.1247171X-RAY DIFFRACTION99.9604
2.159-2.4140.1573030.126525X-RAY DIFFRACTION99.7662
2.414-2.7870.1513040.1315691X-RAY DIFFRACTION99.4361
2.787-3.4110.1632900.1314821X-RAY DIFFRACTION99.3199
3.411-4.8190.1562080.1263766X-RAY DIFFRACTION99.3997
4.819-49.2980.171080.1812127X-RAY DIFFRACTION98.9376
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)
10.1718-0.05130.01880.06640.01490.11350.00280.0160.00940.010.0030.00610.0151-0.0119-0.00580.0046-0.0018-0.00050.01070.00210.0135-21.2757-31.6229-6.7346
20.17780.06660.08820.03240.01010.1769-0.0053-0.04120.031-0.0054-0.00970.0077-0.002-0.02380.0150.0047-0.00130.00260.0185-0.01290.0101-7.63-25.577421.2106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 1201
2X-RAY DIFFRACTION2ALLBBB2 - 1301

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