PDB-7jyb: Binary soak structure of alkanesulfonate monooxygenase MsuD from ...

ID or keywords:

Entry

Database: PDB / ID: 7jyb

Title

Binary soak structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens with FMN

Components

Alkanesulfonate monooxygenase

Keywords

FLAVOPROTEIN / OXIDOREDUCTASE / TIM barrel / flavin monooxygenase

Function / homology

Function and homology information

alkanesulfonate monooxygenase / alkanesulfonate monooxygenase activity / alkanesulfonate catabolic process / nucleotide binding
Similarity search - Function

Biological species

Pseudomonas fluorescens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.76 Å

Authors

Liew, J.J.M. / Dowling, D.P. / El Saudi, I.M.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer.
Authors: Liew, J.J.M. / El Saudi, I.M. / Nguyen, S.V. / Wicht, D.K. / Dowling, D.P.

History

Deposition	Aug 30, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 9, 2021	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jul 7, 2021	Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	7jv3SC 7jw9C 7k14C 7k64C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7jyb-2 7k14-2 7k14-1 7k64-1 7k64-2 7jv3-2 7jw9-d 7jv3-1 3c6c-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#78 - Jun 2006 Luciferase similarity (3)

Deposited unit

A: Alkanesulfonate monooxygenase

B: Alkanesulfonate monooxygenase

C: Alkanesulfonate monooxygenase

D: Alkanesulfonate monooxygenase

E: Alkanesulfonate monooxygenase

F: Alkanesulfonate monooxygenase

G: Alkanesulfonate monooxygenase

H: Alkanesulfonate monooxygenase

hetero molecules

357 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alkanesulfonate monooxygenase

B: Alkanesulfonate monooxygenase

C: Alkanesulfonate monooxygenase

D: Alkanesulfonate monooxygenase

hetero molecules

defined by author
Evidence: gel filtration, Size exclusion chromatography
179 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Alkanesulfonate monooxygenase

F: Alkanesulfonate monooxygenase

G: Alkanesulfonate monooxygenase

H: Alkanesulfonate monooxygenase

hetero molecules

defined by author
178 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.200, 214.380, 95.200
Angle α, β, γ (deg.)	90.000, 119.132, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 0 through 9 or resid 11...
d_2	ens_1	(chain "B" and (resid 0 through 9 or resid 11...
d_3	ens_1	(chain "C" and (resid 0 through 9 or resid 11...
d_4	ens_1	(chain "D" and (resid 0 through 9 or resid 11...
d_5	ens_1	(chain "E" and (resid 0 through 9 or resid 11...
d_6	ens_1	(chain "F" and (resid 0 through 9 or resid 11...
d_7	ens_1	(chain "G" and (resid 0 through 9 or resid 11...
d_8	ens_1	(chain "H" and (resid 0 through 9 or resid 11...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	SER	THR	A	1 - 10
d_1	2	ens_1	GLY	ALA	A	14 - 163
d_1	3	ens_1	TYR	LEU	A	165 - 229
d_1	4	ens_1	VAL	ILE	A	231 - 251
d_1	5	ens_1	SER	ALA	A	302 - 358
d_2	1	ens_1	SER	THR	C	1 - 10
d_2	2	ens_1	GLY	ALA	C	12 - 161
d_2	3	ens_1	TYR	LEU	C	163 - 227
d_2	4	ens_1	VAL	ILE	C	231 - 251
d_2	5	ens_1	SER	ALA	C	272 - 328
d_3	1	ens_1	SER	THR	E	1 - 10
d_3	2	ens_1	GLY	ALA	E	12 - 161
d_3	3	ens_1	TYR	LEU	E	163 - 227
d_3	4	ens_1	VAL	ILE	E	229 - 249
d_3	5	ens_1	SER	ALA	E	300 - 356
d_4	1	ens_1	SER	THR	G	1 - 10
d_4	2	ens_1	GLY	ALA	G	12 - 161
d_4	3	ens_1	TYR	LEU	G	163 - 227
d_4	4	ens_1	VAL	ILE	G	229 - 249
d_4	5	ens_1	SER	ALA	G	269 - 325
d_5	1	ens_1	SER	THR	I	1 - 10
d_5	2	ens_1	GLY	ALA	I	12 - 161
d_5	3	ens_1	TYR	LEU	I	163 - 227
d_5	4	ens_1	VAL	ILE	I	229 - 249
d_5	5	ens_1	SER	ALA	I	300 - 356
d_6	1	ens_1	SER	THR	L	1 - 10
d_6	2	ens_1	GLY	ALA	L	12 - 161
d_6	3	ens_1	TYR	LEU	L	163 - 227
d_6	4	ens_1	VAL	ILE	L	229 - 249
d_6	5	ens_1	SER	ALA	L	267 - 323
d_7	1	ens_1	SER	THR	N	1 - 10
d_7	2	ens_1	GLY	ALA	N	12 - 161
d_7	3	ens_1	TYR	LEU	N	163 - 227
d_7	4	ens_1	VAL	ILE	N	229 - 249
d_7	5	ens_1	SER	ALA	N	266 - 322
d_8	1	ens_1	SER	THR	P	1 - 10
d_8	2	ens_1	GLY	ALA	P	12 - 161
d_8	3	ens_1	TYR	LEU	P	163 - 227
d_8	4	ens_1	VAL	ILE	P	229 - 249
d_8	5	ens_1	SER	LEU	P	280 - 335
d_8	6	ens_1	ALA	ALA	P	346

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.273992723589, -0.182496444803, 0.944257928246), (-0.162824760503, -0.97645957819, -0.141473635455), (0.947848133821, -0.114985824325, -0.29725775922)	-17.4805476488, 3.12948505423, 24.2315485327
2	given	(-0.961059695296, 0.276304832705, 0.00446110988055), (0.276312979223, 0.961066808131, 0.00131446651265), (-0.00392423118375, 0.00249594334786, -0.99998918528)	9.50663089884, -1.21412193079, 44.4219145537
3	given	(-0.307169100155, -0.09672626805, -0.946726556604), (-0.0920944437412, -0.987130713098, 0.130734726416), (-0.94718834312, 0.127345923878, 0.294308101026)	27.2317685013, -3.0676048336, 20.1563297537
4	given	(0.956616010979, 0.0763058200143, 0.281181843956), (0.0746761790272, -0.997070944401, 0.016522715206), (0.281619026034, 0.00519169180757, -0.959512256572)	-57.7942630823, -52.1734346705, -0.605817673432
5	given	(0.514773427969, -0.285095540453, 0.80853500275), (0.181581821109, 0.95794974733, 0.222171834023), (-0.837876100686, 0.0324471016311, 0.54489524268)	-67.522736264, -56.3046194303, -28.4505814438
6	given	(-0.896050897863, 0.337114323042, -0.28887146214), (-0.346681770427, -0.937789704222, -0.0190320968025), (-0.277316675468, 0.0830927424926, 0.957178696823)	-36.1826282171, -49.5784303299, -40.1841509026
7	given	(-0.565732778844, -0.137088955198, -0.813113178656), (0.0455933214827, 0.979374474845, -0.196842289812), (0.823327196185, -0.148432666165, -0.547813902377)	-26.4613886681, -46.5700108703, -12.3706439623

#1: Protein	Alkanesulfonate monooxygenase / FMNH2-dependent aliphatic sulfonate monooxygenase / flavin-dependent methanesulfonate monooxygenase Mass: 44278.887 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: msuD, ssuD, Pfl01_3916 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A1, alkanesulfonate monooxygenase
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₄
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.37 Å³/Da / Density % sol: 48 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, sodium succinate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97949 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 2.76→83.16 Å / Num. obs: 83520 / % possible obs: 98.1 % / Redundancy: 6.193 % / B_iso Wilson estimate: 75.68 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.106 / R_rim(I) all: 0.116 / Χ²: 0.908 / Net I/σ(I): 10.81

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.76-2.83	6.19	0.988	1.83	5925	0.682	1.078	94.1
2.83-2.9	6.166	0.813	2.33	6061	0.744	0.888	99.2
2.9-2.99	6.19	0.643	2.97	5884	0.827	0.702	99
2.99-3.08	5.838	0.491	3.74	5571	0.887	0.539	95.9
3.08-3.18	6.515	0.375	5.12	5545	0.941	0.408	99.5
3.18-3.29	6.502	0.316	5.97	5403	0.958	0.343	99.5
3.29-3.42	6.646	0.246	7.6	5190	0.976	0.267	99.4
3.42-3.56	6.504	0.193	9.45	5033	0.982	0.21	99.5
3.56-3.72	5.919	0.184	10.28	4605	0.979	0.203	95.9
3.72-3.9	6.303	0.13	12.97	4611	0.99	0.142	99.5
3.9-4.11	6.06	0.108	15.23	4392	0.991	0.118	99.1
4.11-4.36	5.661	0.093	16.62	4078	0.993	0.102	98.6
4.36-4.66	5.738	0.081	18.89	3684	0.994	0.089	94.7
4.66-5.03	6.468	0.079	20.76	3647	0.994	0.086	99.3
5.03-5.51	6.236	0.079	20.29	3321	0.994	0.086	99.5
5.51-6.16	6.427	0.079	20.41	3018	0.995	0.086	99.1
6.16-7.12	6.056	0.073	20.63	2667	0.995	0.08	99.1
7.12-8.71	5.718	0.057	22.95	2217	0.996	0.063	96.1
8.71-12.32	6.084	0.047	26.11	1699	0.997	0.051	97.1
12.32-83.16	5.934	0.043	26.12	969	0.998	0.047	97.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7JV3

7jv3

Resolution: 2.76→83.16 Å / SU ML: 0.4312 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.6199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.224	4179	5 %
R_work	0.1798	79319	-
obs	0.182	83498	98.41 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 77.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.76→83.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21115	0	204	48	21367

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	21869
X-RAY DIFFRACTION	f_angle_d	0.5553	29782
X-RAY DIFFRACTION	f_chiral_restr	0.0609	3240
X-RAY DIFFRACTION	f_plane_restr	0.0041	4021
X-RAY DIFFRACTION	f_dihedral_angle_d	16.3531	7869

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.579264446863
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.536040615399
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.640314189234
ens_1	d_5	A	X-RAY DIFFRACTION	Torsion NCS	0.524292600287
ens_1	d_6	A	X-RAY DIFFRACTION	Torsion NCS	0.607992622372
ens_1	d_7	A	X-RAY DIFFRACTION	Torsion NCS	0.615499564028
ens_1	d_8	A	X-RAY DIFFRACTION	Torsion NCS	1.32507936163

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 (%)
2.76-2.79	0.427	122	0.3602	2394	X-RAY DIFFRACTION	88.69
2.79-2.82	0.38	143	0.3207	2662	X-RAY DIFFRACTION	99.19
2.82-2.85	0.3942	143	0.31	2661	X-RAY DIFFRACTION	99.57
2.85-2.89	0.3407	132	0.2787	2656	X-RAY DIFFRACTION	99.01
2.89-2.93	0.305	162	0.2698	2639	X-RAY DIFFRACTION	99.72
2.93-2.97	0.2722	120	0.2513	2706	X-RAY DIFFRACTION	99.05
2.97-3.01	0.2685	135	0.2402	2626	X-RAY DIFFRACTION	99.25
3.01-3.06	0.2587	138	0.2263	2523	X-RAY DIFFRACTION	94.16
3.06-3.1	0.2638	129	0.2283	2616	X-RAY DIFFRACTION	98.11
3.1-3.15	0.2632	145	0.2135	2679	X-RAY DIFFRACTION	99.68
3.15-3.21	0.313	147	0.2194	2694	X-RAY DIFFRACTION	99.72
3.21-3.27	0.2947	128	0.2184	2665	X-RAY DIFFRACTION	99.57
3.27-3.33	0.2638	145	0.2247	2656	X-RAY DIFFRACTION	99.86
3.33-3.4	0.2688	140	0.2082	2704	X-RAY DIFFRACTION	99.51
3.4-3.47	0.2548	141	0.203	2657	X-RAY DIFFRACTION	99.93
3.47-3.55	0.2612	142	0.2054	2695	X-RAY DIFFRACTION	99.68
3.55-3.64	0.244	141	0.1928	2656	X-RAY DIFFRACTION	99.64
3.64-3.74	0.2964	135	0.2453	2510	X-RAY DIFFRACTION	93.66
3.74-3.85	0.2106	137	0.1745	2696	X-RAY DIFFRACTION	99.65
3.85-3.97	0.2253	146	0.1665	2679	X-RAY DIFFRACTION	99.44
3.97-4.12	0.1943	147	0.1605	2657	X-RAY DIFFRACTION	99.72
4.12-4.28	0.2055	127	0.1553	2667	X-RAY DIFFRACTION	98.83
4.28-4.48	0.1991	141	0.1442	2527	X-RAY DIFFRACTION	94.68
4.48-4.71	0.1788	145	0.1356	2625	X-RAY DIFFRACTION	97.74
4.71-5.01	0.1763	135	0.1348	2703	X-RAY DIFFRACTION	99.89
5.01-5.39	0.1829	148	0.1427	2660	X-RAY DIFFRACTION	99.75
5.39-5.94	0.2168	138	0.1541	2706	X-RAY DIFFRACTION	99.86
5.94-6.8	0.1907	142	0.1632	2693	X-RAY DIFFRACTION	99.51
6.8-8.56	0.1796	146	0.1603	2648	X-RAY DIFFRACTION	98.24
8.56-83.16	0.2008	139	0.1673	2659	X-RAY DIFFRACTION	97.09

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	1.14545378022	-0.479453057137	0.359665164168	1.30703594511	-0.242615471929	1.50882705512	0.0327969477745	0.454277487374	0.134137731165	-0.14612090929	-0.266022754386	-0.386516381877	-0.00433300592954	0.569970679521	0.169299033763	0.49588994415	-0.0260156906201	0.0858507829269	0.765689639199	0.122911662442	0.600204722641	29.6958924378	-12.640952054	20.7139097068
2	2.59754740239	0.0351854237295	0.723976573405	1.60803479095	0.613667311258	1.92855482539	0.122974327592	-0.345488061087	0.172382747867	0.401932473516	-0.210818126685	-0.0565875603282	-0.131975785087	-0.107944240236	0.0950156033817	0.700658034978	-0.150619656701	0.00925053536658	0.468960046977	0.0190084528987	0.439650643775	12.7050644673	8.4482851129	46.0648859098
3	1.50897590313	0.576175769358	0.111729545324	1.17803089618	0.0602167043841	3.08328606824	0.0307195012987	-0.319155063027	0.295716993192	0.0930327019872	-0.108381324491	0.287317277922	-0.201338565588	-0.601690897177	0.0594499595949	0.45297247097	0.00685352562412	0.0567063416922	0.604913344275	-0.078973365776	0.552356427286	-22.4841073966	-5.11327838845	23.4898235797
4	3.10240365885	-0.921982844687	0.919229755849	1.84995718382	-0.611025376181	2.33013503518	0.0123716341756	0.549606961016	0.292431325505	-0.277718083245	-0.246243621764	-0.150595157331	-0.216760870181	0.311762346779	0.16230761994	0.636269713787	-0.0274990505165	0.00180613107775	0.52303064063	0.0948230479115	0.464683429718	-0.304987107245	10.2503106158	-1.79594973256
5	0.881597236862	0.393757630374	-0.0804736078003	1.19369961956	0.265925924171	2.19929226602	0.102778714243	-0.107704118439	-0.0235236805613	0.0969944887678	-0.0916029633741	-0.214130351451	0.00629842181457	0.259846153931	0.00252389221379	0.527642736693	-0.0184920220845	-0.0520918946888	0.559006578864	0.0444038642016	0.581768953561	-24.4775576141	-37.015260123	-12.2538477148
6	3.52490865267	0.31519283125	-0.346454653034	1.84795729369	0.661382829294	2.45946663605	0.00367702937074	0.350207965259	-0.133174666912	-0.282819960763	-0.0707400674579	-0.112425497221	0.104593052053	-0.0687193514052	0.0737525893609	0.512867846261	0.0566778093671	-0.00792167748587	0.443073631341	0.0263338412625	0.453453701678	-32.0508268636	-59.1869042896	-40.6678726256
7	2.38090710111	-0.466016680165	0.0556677448308	1.55171587905	-0.340024309412	1.71561988408	0.207683858301	0.360031830055	-0.0788610415289	-0.0255942985493	0.0350471459788	0.68232606006	-0.0328806547553	-0.805489326801	-0.174423372548	0.450693568141	0.0911580006478	-0.0400780380447	0.948529755594	0.0871018302268	0.857040037748	-71.9475158001	-47.2151440929	-28.5399210717
8	2.35368443426	0.880903559358	0.0652082412499	2.93491779819	-0.522519102609	2.76944643722	0.217171032375	-0.182619529605	0.0548752123985	0.345883383027	-0.190938122955	0.23279270053	-0.039495163348	-0.198366377896	-0.028973843015	0.528057453866	-0.077946415479	0.0526286908252	0.507755963163	0.0218861073996	0.46653562872	-56.6821373245	-62.1058951862	1.53309454579

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID
1	1	chain 'A'	A	A - B	0 - 401
2	2	chain 'B'	B	C - D	0 - 401
3	3	chain 'C'	C	E - F	0 - 401
4	4	chain 'D'	D	G - H	0 - 401
5	5	chain 'E'	E	I - K	0 - 501
6	6	chain 'F'	F	L - M	0 - 501
7	7	chain 'G'	G	N - O	0 - 401
8	8	chain 'H'	H	P - Q	0 - 401

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