PDB-6yq3: Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 durin...

ID or keywords:

Entry

Database: PDB / ID: 6yq3

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: 1.57 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	6yq3.cif.gz	192.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6yq3.ent.gz		Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yq/6yq3 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/6yq3	HTTPS FTP

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Related structure data

Related structure data	6ypzC 6yq0C 6yq6C 4ospS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4oso-d 1fx4-1 4zgw-d 4qec-d 1ipe-3 5wul-d 4kwh-d 4m87-d 6t5x-d 4m89-d 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)

Deposited unit

AAA: Monooxygenase

BBB: Monooxygenase

hetero molecules

55.9 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)	87.969, 60.214, 88.308
Angle α, β, γ (deg.)	90.000, 102.458, 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-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2S6PN47
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-P7Q / (3~{R})-8-methoxy-3-methyl-3,6-bis(oxidanyl)-2,4-dihydrobenzo[a]anthracene-1,7,12-trione Mass: 352.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₁₆O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.27 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.57→24.7 Å / Num. obs: 60525 / % possible obs: 98.1 % / Redundancy: 2.9 % / B_iso Wilson estimate: 16.88 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_rim(I) all: 0.064 / Net I/σ(I): 22.5
Reflection shell	Resolution: 1.57→1.61 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.464 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6124 / CC_1/2: 0.818 / R_rim(I) all: 0.566

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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: 1.57→24.696 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.968 / SU B: 2.996 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1663	3027	5.001 %
R_work	0.1421	-	-
all	0.143	-	-
obs	-	60524	96.07 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 16.537 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.832 Å²	0 Å²	-0.522 Å²
2-	-	1.231 Å²	-0 Å²
3-	-	-	-0.153 Å²

Refinement step

Cycle: LAST / Resolution: 1.57→24.696 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3733	0	156	484	4373

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.013	4005
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3734
X-RAY DIFFRACTION	r_angle_refined_deg	2.114	1.668	5471
X-RAY DIFFRACTION	r_angle_other_deg	1.681	1.586	8604
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.293	5	515
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.991	21.078	204
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.637	15	622
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.051	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	546
X-RAY DIFFRACTION	r_chiral_restr_other	1.651	0.2	8
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	4562
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	835
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	858
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	3702
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	2053
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1894
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	375
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.068	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.237	0.2	107
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.161	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	1.291	1.369	2035
X-RAY DIFFRACTION	r_mcbond_other	1.287	1.367	2033
X-RAY DIFFRACTION	r_mcangle_it	1.958	2.048	2542
X-RAY DIFFRACTION	r_mcangle_other	1.953	2.048	2542
X-RAY DIFFRACTION	r_scbond_it	2.448	1.686	1970
X-RAY DIFFRACTION	r_scbond_other	2.447	1.686	1971
X-RAY DIFFRACTION	r_scangle_it	3.823	2.447	2922
X-RAY DIFFRACTION	r_scangle_other	3.822	2.447	2923
X-RAY DIFFRACTION	r_lrange_it	5.555	28.04	18162
X-RAY DIFFRACTION	r_lrange_other	5.432	27.327	17651
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	7796

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 (%)
1.57-1.611	0.239	212	0.218	4253	X-RAY DIFFRACTION	96.9809
1.611-1.655	0.233	211	0.204	4222	X-RAY DIFFRACTION	97.8587
1.655-1.703	0.199	210	0.188	4098	X-RAY DIFFRACTION	97.5986
1.703-1.755	0.197	214	0.17	3934	X-RAY DIFFRACTION	97.3938
1.755-1.813	0.204	198	0.158	3804	X-RAY DIFFRACTION	97.4434
1.813-1.876	0.183	162	0.156	3746	X-RAY DIFFRACTION	97.069
1.876-1.947	0.182	177	0.151	3560	X-RAY DIFFRACTION	96.8888
1.947-2.027	0.174	184	0.142	3463	X-RAY DIFFRACTION	97.0721
2.027-2.117	0.171	163	0.133	3256	X-RAY DIFFRACTION	96.6365
2.117-2.22	0.183	158	0.134	3150	X-RAY DIFFRACTION	95.9675
2.22-2.34	0.155	158	0.124	2943	X-RAY DIFFRACTION	95.5624
2.34-2.481	0.165	133	0.116	2799	X-RAY DIFFRACTION	95.5983
2.481-2.653	0.155	174	0.127	2593	X-RAY DIFFRACTION	95.348
2.653-2.865	0.14	142	0.13	2444	X-RAY DIFFRACTION	95.3188
2.865-3.138	0.164	114	0.137	2253	X-RAY DIFFRACTION	94.7938
3.138-3.507	0.164	127	0.135	1987	X-RAY DIFFRACTION	93.9138
3.507-4.048	0.158	98	0.127	1761	X-RAY DIFFRACTION	93.6052
4.048-4.953	0.125	85	0.122	1494	X-RAY DIFFRACTION	92.3392
4.953-6.987	0.149	69	0.163	1134	X-RAY DIFFRACTION	90.5873
6.987-24.696	0.152	38	0.161	603	X-RAY DIFFRACTION	84.5646

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	0.2156	-0.1046	0.1361	0.1068	0.014	0.217	-0.0127	0.0501	0.032	0.0143	-0.0137	-0.0046	-0.0002	0.0332	0.0264	0.0023	-0.0001	0.001	0.0221	0.0167	0.0131	-1.892	1.6889	21.9542
2	0.1945	0.0467	0.0552	0.051	-0.0208	0.165	0.0084	-0.0169	0.0204	-0.009	0.0055	0.0019	0.0254	0.0208	-0.0139	0.0053	0.0008	-0.0022	0.0154	-0.005	0.0162	11.8364	-4.7191	49.7031

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	2 - 901
2	X-RAY DIFFRACTION	2	ALL	BBB	2 - 701

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