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

ID or keywords:

Entry

Database: PDB / ID: 6ypz

Title

Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis

Components

Monooxygenase

Keywords

ANTIBIOTIC / lugdunomycin / keto-reduction / short chain alcohol reductase / Rossmann fold

Function / homology

Function and homology information

FAD binding / monooxygenase activity
Similarity search - Function

Biological species

Streptomyces sp. QL37 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.08 Å

Authors

Xiao, X. / Elsayed, S.S. / Wu, C. / van der Heul, H. / Prota, A. / Huang, J. / Guo, R. / Abrahams, J.P. / van Wezel, G.P.

Citation

Journal: 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

Deposition	Apr 16, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2020	Group: 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 1.2	Jan 24, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ypz.cif.gz	191.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6ypz_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6ypz_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6ypz_validation.xml.gz	26.5 KB	Display
Data in CIF	6ypz_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypz ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypz	HTTPS FTP

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Related structure data

Related structure data	6yq0C 6yq3C 6yq6C 4ospS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6yq0-d 2ntv-d 4nbv-d 4qed-d 2ntj-d 4oso-d 6yq3-d 1pv2-1 3wog-d 5dtt-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

AAA: Monooxygenase

BBB: Monooxygenase

hetero molecules

56 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	5
Space group name H-M	I121

Noncrystallographic symmetry (NCS)

NCS domain: (Details: Chains AAA BBB)

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.12 Å³/Da / Density % sol: 42 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.08→49.3 Å / Num. obs: 428985 / % possible obs: 95.4 % / Redundancy: 3.1 % / B_iso Wilson estimate: 12.94 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.054 / R_rim(I) all: 0.064 / R_sym value: 0.054 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.08→1.108 Å / Redundancy: 3 % / R_merge(I) obs: 0.679 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 67732 / CC_1/2: 0.648 / R_rim(I) all: 0.827 / R_sym value: 0.679 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4osp

4osp

Resolution: 1.08→49.298 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.974 / WR_factor R_free: 0.15 / WR_factor R_work: 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

	R_factor	Num. reflection	% reflection
R_free	0.1653	9588	5.009 %
R_work	0.1457	181839	-
all	0.147	-	-
obs	-	191427	99.91 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 11.858 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.316 Å²	0 Å²	-0.244 Å²
2-	-	0.492 Å²	0 Å²
3-	-	-	-0.062 Å²

Refinement step

Cycle: LAST / Resolution: 1.08→49.298 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3730	0	158	508	4396

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.013	4028
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3818
X-RAY DIFFRACTION	r_angle_refined_deg	2.215	1.654	5468
X-RAY DIFFRACTION	r_angle_other_deg	1.654	1.574	8803
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.158	5	524
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.615	20.952	210
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.422	15	636
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.115	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	549
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	4577
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	842
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	885
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	3795
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2040
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1958
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.225	0.2	372
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.318	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.269	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.285	0.2	117
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.171	0.2	36
X-RAY DIFFRACTION	r_mcbond_it	1.114	0.904	2044
X-RAY DIFFRACTION	r_mcbond_other	1.101	0.902	2042
X-RAY DIFFRACTION	r_mcangle_it	1.658	1.36	2557
X-RAY DIFFRACTION	r_mcangle_other	1.651	1.359	2557
X-RAY DIFFRACTION	r_scbond_it	2.117	1.141	1984
X-RAY DIFFRACTION	r_scbond_other	2.117	1.142	1985
X-RAY DIFFRACTION	r_scangle_it	3.056	1.622	2900
X-RAY DIFFRACTION	r_scangle_other	3.056	1.623	2901
X-RAY DIFFRACTION	r_lrange_it	4.235	19.095	18116
X-RAY DIFFRACTION	r_lrange_other	4.057	18.476	17668
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	7811

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.08-1.108	0.266	669	0.27	13457	X-RAY DIFFRACTION	99.9646
1.108-1.138	0.235	730	0.236	13024	X-RAY DIFFRACTION	99.9346
1.138-1.171	0.223	677	0.211	12678	X-RAY DIFFRACTION	99.9701
1.171-1.207	0.212	668	0.202	12363	X-RAY DIFFRACTION	99.9923
1.207-1.247	0.189	646	0.187	11921	X-RAY DIFFRACTION	99.9841
1.247-1.291	0.189	596	0.175	11593	X-RAY DIFFRACTION	99.9672
1.291-1.339	0.17	554	0.158	11216	X-RAY DIFFRACTION	99.983
1.339-1.394	0.184	539	0.155	10821	X-RAY DIFFRACTION	99.9736
1.394-1.456	0.158	554	0.142	10280	X-RAY DIFFRACTION	100
1.456-1.527	0.164	553	0.136	9877	X-RAY DIFFRACTION	99.9808
1.527-1.61	0.148	509	0.128	9364	X-RAY DIFFRACTION	99.9797
1.61-1.707	0.142	458	0.125	8896	X-RAY DIFFRACTION	100
1.707-1.825	0.138	436	0.121	8375	X-RAY DIFFRACTION	99.9886
1.825-1.971	0.149	385	0.125	7824	X-RAY DIFFRACTION	99.9878
1.971-2.159	0.142	399	0.124	7171	X-RAY DIFFRACTION	99.9604
2.159-2.414	0.157	303	0.12	6525	X-RAY DIFFRACTION	99.7662
2.414-2.787	0.151	304	0.131	5691	X-RAY DIFFRACTION	99.4361
2.787-3.411	0.163	290	0.131	4821	X-RAY DIFFRACTION	99.3199
3.411-4.819	0.156	208	0.126	3766	X-RAY DIFFRACTION	99.3997
4.819-49.298	0.17	108	0.181	2127	X-RAY DIFFRACTION	98.9376

Refinement TLS params.

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

ID	L11 (°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)
1	0.1718	-0.0513	0.0188	0.0664	0.0149	0.1135	0.0028	0.016	0.0094	0.01	0.003	0.0061	0.0151	-0.0119	-0.0058	0.0046	-0.0018	-0.0005	0.0107	0.0021	0.0135	-21.2757	-31.6229	-6.7346
2	0.1778	0.0666	0.0882	0.0324	0.0101	0.1769	-0.0053	-0.0412	0.031	-0.0054	-0.0097	0.0077	-0.002	-0.0238	0.015	0.0047	-0.0013	0.0026	0.0185	-0.0129	0.0101	-7.63	-25.5774	21.2106

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 1201
2	X-RAY DIFFRACTION	2	ALL	BBB	2 - 1301

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