PDB-7s2l: Crystal structure of sulfonamide resistance enzyme Sul3 apoenzyme

ID or keywords:

Entry

Database: PDB / ID: 7s2l

Title

Crystal structure of sulfonamide resistance enzyme Sul3 apoenzyme

Components

Sul3

Keywords

TRANSFERASE / IM barrel / alpha beta protein / antibiotic resistance / sulfonamides / structural genomics / CSGID / Center for Structural genomics of infectious diseases / NIAID / National Institute of Allergy and Infectious Diseases

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 Å

Authors

Stogios, P.J. / Venkatesan, M. / Michalska, K. / Mesa, N. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics.
Authors: Venkatesan, M. / Fruci, M. / Verellen, L.A. / Skarina, T. / Mesa, N. / Flick, R. / Pham, C. / Mahadevan, R. / Stogios, P.J. / Savchenko, A.

History

Deposition	Sep 3, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7s2l.cif.gz	461.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7s2l.ent.gz	342.1 KB	Display	PDB format
PDBx/mmJSON format	7s2l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7s2l_validation.pdf.gz	493.2 KB	Display	wwPDB validaton report
Full document	7s2l_full_validation.pdf.gz	515.8 KB	Display
Data in XML	7s2l_validation.xml.gz	39.6 KB	Display
Data in CIF	7s2l_validation.cif.gz	53.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/7s2l ftp://data.pdbj.org/pub/pdb/validation_reports/s2/7s2l	HTTPS FTP

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Related structure data

Related structure data	7s2iC 7s2jC 7s2kC 7s2mC 7tq1C 8scdC 1aj0S 7s2o PDB Unreleased entry C: citing same article (ref.) S: Starting model for refinement
Other databases	TargetTrack: IDP97059

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Sul3

B: Sul3

C: Sul3

D: Sul3

hetero molecules

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

1

A: Sul3

hetero molecules

C: Sul3

hetero molecules

defined by author
Evidence: gel filtration
59.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sul3

hetero molecules

D: Sul3

hetero molecules

defined by author
Evidence: gel filtration
58.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.804, 123.804, 434.424
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22
Space group name Hall	P6₅2(x,y,z+1/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: x-y,-y,-z #7: -x,-x+y,-z+1/3 #8: -x,-y,z+1/2 #9: y,x,-z+2/3 #10: -y,-x,-z+1/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+5/6

#1: Protein	Sul3 Mass: 28946.377 Da / Num. of mol.: 4 / Mutation: E94A/Q95A/K96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: Sul3 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 128 / 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: 4.14 Å³/Da / Density % sol: 70.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% w/v PEG400, 1% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.8→30 Å / Num. obs: 49842 / % possible obs: 100 % / Redundancy: 27.2 % / B_iso Wilson estimate: 64.79 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.311 / R_pim(I) all: 0.06 / Net I/σ(I): 16.38
Reflection shell	Resolution: 2.8→2.85 Å / Redundancy: 19.7 % / R_merge(I) obs: 3.63 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 2422 / CC_1/2: 0.587 / R_pim(I) all: 0.815 / % possible all: 100

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Processing

Software

Name	Version	Classification
phenix.refine	1.19.2_4158	refinement
PHENIX	1.19.2_4158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1AJ0

1aj0

Resolution: 2.79→30 Å / SU ML: 0.4239 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.7487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.27	3687	4.02 %
R_work	0.226	87925	-
obs	0.2277	49650	99.39 %

Solvent computation

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

Displacement parameters

B_iso mean: 76.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.79→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7959	0	91	128	8178

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0051	8162
X-RAY DIFFRACTION	f_angle_d	0.7708	11000
X-RAY DIFFRACTION	f_chiral_restr	0.0486	1281
X-RAY DIFFRACTION	f_plane_restr	0.0059	1390
X-RAY DIFFRACTION	f_dihedral_angle_d	23.21	3039

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 (%)
2.79-2.83	0.4036	122	0.4039	3004	X-RAY DIFFRACTION	88.08
2.83-2.87	0.4267	145	0.3658	3424	X-RAY DIFFRACTION	99.78
2.87-2.91	0.4182	140	0.3512	3357	X-RAY DIFFRACTION	99.8
2.91-2.95	0.3477	145	0.3468	3455	X-RAY DIFFRACTION	99.92
2.95-3	0.4001	145	0.3467	3345	X-RAY DIFFRACTION	100
3-3.05	0.3759	138	0.3398	3401	X-RAY DIFFRACTION	99.89
3.05-3.1	0.3819	141	0.3279	3431	X-RAY DIFFRACTION	99.86
3.1-3.16	0.3406	144	0.3113	3401	X-RAY DIFFRACTION	99.92
3.16-3.22	0.4228	139	0.3054	3348	X-RAY DIFFRACTION	99.74
3.22-3.29	0.3409	145	0.3001	3422	X-RAY DIFFRACTION	99.92
3.29-3.36	0.3543	147	0.286	3409	X-RAY DIFFRACTION	99.69
3.36-3.43	0.3476	143	0.2717	3386	X-RAY DIFFRACTION	99.52
3.43-3.52	0.3024	138	0.257	3386	X-RAY DIFFRACTION	99.77
3.52-3.62	0.3652	144	0.2782	3371	X-RAY DIFFRACTION	99.8
3.62-3.72	0.2866	141	0.2543	3403	X-RAY DIFFRACTION	99.77
3.72-3.84	0.2655	145	0.236	3377	X-RAY DIFFRACTION	99.58
3.84-3.98	0.2824	144	0.2102	3410	X-RAY DIFFRACTION	99.92
3.98-4.14	0.2445	138	0.193	3422	X-RAY DIFFRACTION	99.94
4.14-4.33	0.2434	141	0.1772	3374	X-RAY DIFFRACTION	99.91
4.33-4.55	0.209	144	0.1762	3409	X-RAY DIFFRACTION	99.89
4.55-4.84	0.2208	140	0.1702	3371	X-RAY DIFFRACTION	99.97
4.84-5.21	0.1973	150	0.1683	3411	X-RAY DIFFRACTION	99.97
5.21-5.73	0.2619	134	0.185	3412	X-RAY DIFFRACTION	99.97
5.73-6.55	0.2582	142	0.2045	3416	X-RAY DIFFRACTION	99.92
6.55-8.22	0.2017	149	0.1875	3397	X-RAY DIFFRACTION	99.94
8.22-30	0.1823	143	0.1688	3383	X-RAY DIFFRACTION	99.66

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	4.82144177796	1.55253457546	0.385332287096	1.58126854126	-1.38705204401	2.95781781703	-0.184158104399	-0.0636506537112	0.848862153916	-0.293571369966	0.400521692796	0.266706940812	-1.1195733441	-0.571350584216	2.60265897946E-7	0.764267089337	0.0382690628309	0.0691927823493	0.901968480043	-0.0010751462078	0.693299739166	-56.3988862013	35.9514133945	-13.6378676554
2	3.47767332409	0.186904463207	-1.39405348442	0.987595535345	-0.459967643956	2.7636178203	-0.0358719820497	-0.262896875082	-0.126078815727	0.136062074753	-0.143174700918	-0.0644622030772	0.00103057522473	0.185889406699	-4.65884606114E-9	0.481280345437	-0.0558814886303	0.0511604792501	0.554857612527	0.0464971950189	0.607494740637	-44.6788431057	28.0913147235	-7.2936473348
3	2.63173921192	-0.410681348825	0.0261429170774	1.10532883416	0.360651392063	1.1501320507	-0.165682556795	-0.550631142284	0.681191515661	0.563729235953	0.124849189763	-0.0211632320273	-1.11580718145	0.553847744589	-0.000261457963761	1.19809060537	-0.157182064379	0.115872825467	1.12069216228	-0.144586504524	0.731335027986	-67.220006679	33.7913584835	26.3589235852
4	2.87328031471	0.223495036244	-1.26668298372	0.899157302728	-0.319185669713	3.73513719242	0.0185281288527	-0.0721324879985	-0.205413015171	0.0577668296433	0.0219004097502	0.0611831383484	-0.340373019544	0.128875220902	3.09233669893E-9	0.587671178491	-0.0129883402092	0.103646477215	0.475417059422	-0.0248468693416	0.638023188685	-77.6864963133	27.525616814	19.4101876383
5	2.07758399033	0.352407804981	-0.233242583068	1.10816123644	1.15393614671	1.26631085637	0.184720250703	-0.77347811555	-0.584688349381	0.0602553387392	0.448786529671	0.954166124002	0.559741142574	-0.0168199808308	-3.00559180643E-6	0.851485334446	-0.058450636412	-0.0290878781592	0.769489539822	0.0532658842685	0.716547132285	-44.9543667353	55.1386257381	-22.19642873
6	1.32452087044	-0.51820570444	0.910966467954	1.58948346035	0.239864693751	0.798429661373	-0.238248030434	0.233724408916	-0.633901287173	0.316985684101	-0.00858656362286	0.327963509766	0.592274259544	-0.901345945846	-0.0231281906297	0.729134844209	-0.149489334017	0.0147947845614	0.821946257438	-0.0510607952932	0.702205505377	-43.3242709168	55.3144979801	-23.460708168
7	0.836370422743	-0.856371735132	0.051805579427	1.6052895773	0.510097654828	0.391957413298	-0.228149533458	-0.466598482381	-0.137445154871	0.593899329007	0.00774829419556	0.078773417477	-0.241375062431	0.120120776761	-3.223832945E-7	0.743171750938	-0.0383390848359	-0.00556692670942	0.655847123402	-0.00235589529471	0.610417081738	-45.8857550452	63.9644906559	-14.5374181281
8	2.31649339945	0.795208971924	-0.307366187447	2.58543643883	1.22057010811	3.13384348527	0.051040121175	-0.185404922435	0.159412108032	0.30551574098	-0.189378359368	0.390394689557	-0.24167235154	-0.70236275139	-2.57456724779E-8	0.619711871545	-0.00138990989224	-0.0168871178808	0.755777850713	-0.00808966763272	0.665579724007	-61.0738220202	67.3515094087	-27.8385044014
9	2.69701686849	-0.229486852232	0.788637827105	1.92564171112	-1.28528998396	1.13521199065	0.01013372003	-0.06280847495	-0.701486433475	-0.265291772563	-0.411550897476	-0.625694582888	0.366860666452	0.0897971230646	-0.0022666023479	0.74814374673	0.118615437769	0.0889774364414	0.810679135805	0.213057009595	0.860219106107	-75.5785449449	57.5177099998	12.6379610586
10	2.42557810819	-0.25218082323	0.589175267172	1.29096213404	-0.164004991181	2.5545504953	0.105987686913	0.278493407987	0.312158124189	-0.116096619497	-0.301813903559	-0.352261647326	-0.213343586902	0.567646555099	-4.62441407671E-9	0.638736841228	0.0120594583488	0.0490242355721	0.941026876189	0.199187145253	0.743137517839	-65.0531631127	67.3957703554	13.0322695616

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -1 through 57 )	A	A	-1 - 57	1 - 59
2	2	chain 'A' and (resid 58 through 263 )	A	A	58 - 263	60 - 265
3	3	chain 'B' and (resid 0 through 57 )	B	E	0 - 57	1 - 54
4	4	chain 'B' and (resid 58 through 263 )	B	E	58 - 263	55 - 260
5	5	chain 'C' and (resid 0 through 20 )	C	F	0 - 20	1 - 21
6	6	chain 'C' and (resid 21 through 54 )	C	F	21 - 54	22 - 55
7	7	chain 'C' and (resid 55 through 111 )	C	F	55 - 111	56 - 112
8	8	chain 'C' and (resid 112 through 263 )	C	F	112 - 263	113 - 264
9	9	chain 'D' and (resid 0 through 54 )	D	J	0 - 54	1 - 46
10	10	chain 'D' and (resid 57 through 263 )	D	J	57 - 263	47 - 249

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