PDB-5v8d: Structure of Bacillus cereus PatB1 with sulfonyl adduct

ID or keywords:

Entry

Database: PDB / ID: 5v8d

Title

Structure of Bacillus cereus PatB1 with sulfonyl adduct

Components

(Bacillus cereus PatB1) x 2

Keywords

TRANSFERASE / acetyltransferase / cell wall / SGNH hydrolase-like

Function / homology

DHHW protein / DHHW protein / membrane / AlgX/AlgJ SGNH hydrolase-like domain-containing protein

Function and homology information

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.001 Å

Authors

Sychantha, D. / Little, D.J. / Chapman, R.N. / Boons, G.J. / Robinson, H. / Howell, P.L. / Clarke, A.J.

Funding support

Canada, 2items

Citation

Journal: Nat. Chem. Biol. / Year: 2018
Title: PatB1 is an O-acetyltransferase that decorates secondary cell wall polysaccharides.
Authors: Sychantha, D. / Little, D.J. / Chapman, R.N. / Boons, G.J. / Robinson, H. / Howell, P.L. / Clarke, A.J.

History

Deposition	Mar 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 6, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 20, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5v8d.cif.gz	498.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5v8d.ent.gz	407.9 KB	Display	PDB format
PDBx/mmJSON format	5v8d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5v8d_validation.pdf.gz	485.1 KB	Display	wwPDB validaton report
Full document	5v8d_full_validation.pdf.gz	496.6 KB	Display
Data in XML	5v8d_validation.xml.gz	50.1 KB	Display
Data in CIF	5v8d_validation.cif.gz	71.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v8/5v8d ftp://data.pdbj.org/pub/pdb/validation_reports/v8/5v8d	HTTPS FTP

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Related structure data

Related structure data	5v8eC C: citing same article (ref.)
Similar structure data	1h51-d 1gvo-d 1snz-2 1qns-d 2p9w-d 2ciw-d 1gvq-d 4uzl-1 5v8e-2 3wh9-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5v8eC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bacillus cereus PatB1

B: Bacillus cereus PatB1

C: Bacillus cereus PatB1

D: Bacillus cereus PatB1

hetero molecules

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

1

A: Bacillus cereus PatB1

hetero molecules

defined by author&software
Evidence: gel filtration
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Bacillus cereus PatB1

hetero molecules

defined by author&software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Bacillus cereus PatB1

hetero molecules

defined by author&software
42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Bacillus cereus PatB1

hetero molecules

defined by author&software
42.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	125.467, 110.475, 99.156
Angle α, β, γ (deg.)	90.00, 108.15, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-597- HOH
2	1	C-582- HOH
3	1	D-603- HOH

#1: Protein	Bacillus cereus PatB1 / Uncharacterized protein Mass: 42057.078 Da / Num. of mol.: 2 / Fragment: UNP residues 33-396 / Mutation: K232A, K233A, E234A, K300A, Q301A, K302A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria) Strain: ATCC 10987 / NRS 248 / Gene: BCE_0974 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Shuffle / References: UniProt: Q73CU0
#2: Protein	Bacillus cereus PatB1 Mass: 41977.016 Da / Num. of mol.: 2 / Fragment: UNP residues 33-396 / Mutation: K232A, K233A, E234A, K300A, Q301A, K302A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 10987 / NRS 248) (bacteria) Strain: ATCC 10987 / NRS 248 / Gene: BCE_0974 / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Shuffle / References: UniProt: Q73CU0
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 1.94 Å³/Da / Density % sol: 36.69 % / Description: Cubes
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.8-1.9 M ammonium sulfate and 0.1 M BIS-TRIS pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.08 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 86279 / % possible obs: 100 % / Redundancy: 7.8 % / R_merge(I) obs: 0.137 / Net I/σ(I): 15.7
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8342 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.001→47.653 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27

	R_factor	Num. reflection	% reflection
R_free	0.2718	3946	2.32 %
R_work	0.2211	-	-
obs	0.2223	86245	99.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.001→47.653 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9488	0	55	694	10237

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9776
X-RAY DIFFRACTION	f_angle_d	1.117	13296
X-RAY DIFFRACTION	f_dihedral_angle_d	13.714	3430
X-RAY DIFFRACTION	f_chiral_restr	0.042	1436
X-RAY DIFFRACTION	f_plane_restr	0.005	1712

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 (%)
2.0007-2.0251	0.3192	127	0.2854	5389	X-RAY DIFFRACTION	90
2.0251-2.0507	0.3126	142	0.2689	5974	X-RAY DIFFRACTION	100
2.0507-2.0777	0.2823	140	0.2685	5932	X-RAY DIFFRACTION	100
2.0777-2.1061	0.2924	142	0.2584	5989	X-RAY DIFFRACTION	100
2.1061-2.1362	0.295	142	0.2518	5915	X-RAY DIFFRACTION	100
2.1362-2.1681	0.2931	142	0.2489	5921	X-RAY DIFFRACTION	100
2.1681-2.202	0.2845	144	0.2447	6055	X-RAY DIFFRACTION	100
2.202-2.2381	0.2722	139	0.2406	5848	X-RAY DIFFRACTION	100
2.2381-2.2767	0.3227	142	0.2418	6015	X-RAY DIFFRACTION	100
2.2767-2.3181	0.2543	142	0.2398	5985	X-RAY DIFFRACTION	100
2.3181-2.3627	0.3208	144	0.2292	5940	X-RAY DIFFRACTION	100
2.3627-2.4109	0.2818	141	0.223	5914	X-RAY DIFFRACTION	100
2.4109-2.4633	0.2267	144	0.2278	6039	X-RAY DIFFRACTION	100
2.4633-2.5206	0.2442	141	0.2289	5947	X-RAY DIFFRACTION	100
2.5206-2.5836	0.2718	141	0.2151	5911	X-RAY DIFFRACTION	100
2.5836-2.6535	0.2712	144	0.226	5976	X-RAY DIFFRACTION	100
2.6535-2.7316	0.2412	137	0.2205	5930	X-RAY DIFFRACTION	100
2.7316-2.8197	0.2621	139	0.2297	5941	X-RAY DIFFRACTION	100
2.8197-2.9205	0.3057	144	0.2296	6009	X-RAY DIFFRACTION	100
2.9205-3.0374	0.2989	138	0.214	5923	X-RAY DIFFRACTION	100
3.0374-3.1756	0.2558	140	0.2288	5956	X-RAY DIFFRACTION	100
3.1756-3.343	0.2823	144	0.2156	6033	X-RAY DIFFRACTION	100
3.343-3.5524	0.3047	143	0.2087	5860	X-RAY DIFFRACTION	100
3.5524-3.8265	0.2621	143	0.1978	5958	X-RAY DIFFRACTION	100
3.8265-4.2114	0.2238	140	0.1909	5960	X-RAY DIFFRACTION	100
4.2114-4.8203	0.233	142	0.1783	5947	X-RAY DIFFRACTION	100
4.8203-6.0711	0.2679	141	0.2212	5942	X-RAY DIFFRACTION	100
6.0711-47.6661	0.3194	144	0.2576	5940	X-RAY DIFFRACTION	99

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	2.5478	-0.6903	0.1576	1.6513	-0.4523	2.1883	0.0352	-0.2561	-0.1891	0.143	-0.0083	0.1604	0.1136	-0.0741	-0.0467	0.183	-0.0578	-0.0007	0.1756	0.0221	0.2452	231.5373	-11.2198	120.7088
2	4.1206	-1.9728	-1.3753	4.6359	0.3794	0.6903	0.0301	0.1244	-0.4707	0.1433	0.0789	-0.364	0.2019	0.3669	-0.0713	0.2239	0.0121	0.0023	0.1782	0.0799	0.2726	246.7232	-17.0605	109.8519
3	1.9766	-0.4087	0.3782	3.2579	-0.3701	3.2174	-0.0431	0.0534	0.0275	-0.0088	-0.0345	-0.1341	-0.037	0.2084	0.0517	0.1033	-0.0026	0.0081	0.2071	0.0011	0.2392	245.8921	-3.6993	106.5625
4	1.9114	-0.0281	0.3779	1.4545	0.2238	5.355	0.0744	0.1411	0.4277	-0.0263	0.0337	0.0692	-0.4399	-0.1462	-0.0764	0.1357	-0.0006	0.0308	0.142	0.02	0.289	232.648	2.5344	109.2901
5	4.0902	-5.0219	2.7742	6.236	-3.3363	3.3969	-0.4463	-0.4903	-0.2286	0.6173	0.6505	0.3165	-0.115	-0.3501	-0.1988	0.4173	-0.0686	-0.0221	0.5694	0.036	0.3028	232.5366	46.221	135.3064
6	2.5698	-0.72	-0.3243	2.0935	0.4469	1.7926	0.0176	-0.1629	0.0577	0.1855	-0.0388	-0.0947	-0.0274	0.1144	-0.003	0.1805	-0.052	-0.0198	0.1933	-0.0088	0.2789	242.4378	47.4616	120.664
7	9.5767	-4.0052	-0.5009	3.1788	0.7222	0.4801	0.2361	0.3838	0.6229	-0.3145	-0.0513	-0.2346	-0.0588	0.1201	-0.1696	0.2834	-0.0246	0.0187	0.2053	0.0114	0.3128	233.9125	54.7339	105.8874
8	7.2035	-0.6368	-2.2616	5.9153	-2.9311	2.704	0.0495	-0.75	0.0929	0.7173	0.4668	0.4539	-0.1898	-0.8407	-0.4068	0.2682	0.0011	0.0254	0.4444	0.0127	0.4475	218.2175	52.1174	117.6975
9	4.8561	2.8579	-2.2179	6.5587	0.7682	3.0706	-0.1847	0.2218	-0.3872	-0.7767	0.1045	0.5241	0.0015	-0.4961	0.0802	0.1939	0.0015	-0.0381	0.3356	0.0274	0.2801	222.4559	37.4208	102.4778
10	4.9536	-1.9365	-1.9389	2.7786	1.7252	3.7938	-0.0728	0.1669	-0.0574	0.0326	0.0125	0.0524	0.1142	-0.1498	0.0394	0.1711	-0.0554	-0.0314	0.1782	0.0136	0.2699	227.742	42.0209	108.0252
11	2.2446	0.5637	-0.0224	1.8757	0.1185	5.9926	0.0474	0.1391	-0.3887	-0.0607	-0.0339	-0.3176	0.4146	0.1508	-0.0048	0.1589	0.0144	0.001	0.1483	0.007	0.3105	239.619	34.4225	109.3038
12	6.1785	4.662	0.9403	6.6539	0.5202	3.473	0.0116	-0.5904	0.0064	0.2511	-0.0747	0.5025	0.5549	0.2695	0.0958	0.4345	-0.0369	0.0061	0.4686	-0.0468	0.3063	267.3367	17.6264	134.6752
13	4.5168	2.3605	-3.4629	4.0837	-3.3634	5.9833	0.0752	-0.4158	0.4182	0.2273	-0.2304	-0.2408	-0.7749	0.6931	0.1466	0.2698	-0.0741	-0.0046	0.2478	-0.052	0.4975	277.7885	37.3714	117.3011
14	2.1106	0.669	0.169	2.1351	-0.0467	2.9637	0.0476	-0.2007	0.3101	0.205	0.02	0.1943	-0.1611	-0.2671	-0.0705	0.1649	0.0219	0.0298	0.2161	-0.0264	0.2974	261.9992	25.1204	119.8156
15	4.4328	2.1441	-0.5181	2.5512	0.8074	1.445	-0.0127	-0.0781	-0.0768	0.2653	0.2855	0.6884	0.2422	-0.5063	-0.2271	0.2418	-0.0244	0.1002	0.1771	-0.0574	0.276	260.0329	10.9346	112.9994
16	7.9255	0.8524	-1.238	0.6137	-0.6706	0.6102	-0.1651	0.6465	-0.556	-0.1011	0.049	-0.0753	0.2035	-0.0989	0.0825	0.2804	-0.0718	-0.0242	0.2541	-0.0797	0.3733	272.267	8.5753	104.1571
17	2.1215	0.4131	-0.6129	2.9897	-0.2545	2.7532	0.0049	0.0921	-0.142	-0.1228	0.0528	-0.1665	0.0332	0.2127	-0.0585	0.1345	-0.0124	-0.0212	0.1829	-0.01	0.2558	275.0924	19.5289	108.937
18	1.918	-2.0856	-0.054	9.852	0.4814	0.5466	-0.1178	0.3287	-0.0804	-0.1859	0.2265	0.3183	-0.2743	0.4339	0.0095	0.4266	0.0741	0.0494	0.5478	-0.0299	0.2089	235.8828	19.0434	53.6581
19	2.2242	-1.2487	-0.3414	2.3468	0.3583	2.6624	0.0328	0.1692	-0.307	-0.1443	-0.0262	0.1226	0.1508	-0.1477	-0.0479	0.1549	-0.0371	-0.02	0.1693	-0.0104	0.2483	232.7952	9.5425	69.2323
20	3.0649	-3.4118	1.1799	6.4064	-1.8784	3.1475	-0.4239	-0.4446	-0.367	0.5118	0.5488	0.5599	0.0371	-0.5363	-0.1595	0.2504	0.0779	0.0339	0.2477	0.0527	0.3019	225.9127	18.822	84.8314
21	5.2156	-1.4881	0.8029	3.0218	-0.5842	1.5089	-0.1521	0.0467	0.5485	-0.0467	-0.0615	-0.1211	-0.2294	-0.0047	0.2059	0.2932	-0.002	0.0119	0.1667	-0.0259	0.2695	238.7155	29.6585	77.3436
22	2.2275	-0.3023	0.6381	2.7697	-0.0324	3.7995	-0.0739	-0.1912	0.0567	0.2225	0.0722	-0.1675	0.1397	0.2241	-0.0236	0.1319	0.0222	-0.0007	0.1476	-0.0123	0.237	243.8852	13.2444	80.6145

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 93 through 222 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 223 through 270 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 271 through 349 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 350 through 396 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 80 through 110 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 111 through 204 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 205 through 241 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 242 through 270 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 271 through 294 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 295 through 349 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 350 through 396 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 83 through 110 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 111 through 130 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 131 through 222 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 223 through 264 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 265 through 294 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 295 through 396 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 84 through 110 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 111 through 222 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 223 through 241 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 242 through 321 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 322 through 396 )

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