PDB-22ao: Crystal structure of Bacillus cereus GmaR in the apo form

ID or keywords:

Entry

Database: PDB / ID: 22ao

Title

Crystal structure of Bacillus cereus GmaR in the apo form

Components

GmaR

Keywords

TRANSFERASE / glycosyltransferase

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Oh, H.B. / Lee, S.J. / Yoon, S.I.

Funding support

Korea, Republic Of, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2026
Title: Bacillus cereus GmaR glycosylates flagellin through a unique structural motif but is uncoupled from MogR regulation.
Authors: Oh, H.B. / Lee, S.J. / Yoon, S.I.

History

Deposition	Jan 5, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 22, 2026	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2026	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	22ao.cif.gz	212.5 KB	Display	PDBx/mmCIF format
PDB format	pdb22ao.ent.gz	171.5 KB	Display	PDB format
PDBx/mmJSON format	22ao.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2a/22ao ftp://data.pdbj.org/pub/pdb/validation_reports/2a/22ao	HTTPS FTP

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Related structure data

Related structure data	22apC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: GmaR

B: GmaR

C: GmaR

69.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GmaR

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

2

B: GmaR

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

3

C: GmaR

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

Unit cell

Length a, b, c (Å)	82.596, 82.596, 193.971
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	GmaR Mass: 23147.973 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: WP_073529963.1, residues 1-198; The first six residues in the sample sequence (GSAKDP) is from the plasmid. Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.38 Å³/Da / Density % sol: 48.36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, Tris

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.8→30 Å / Num. obs: 16959 / % possible obs: 97.6 % / Redundancy: 4.9 % / CC_1/2: 0.997 / Net I/σ(I): 28.8
Reflection shell	Resolution: 2.8→2.85 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.9 / Num. unique obs: 836 / CC_1/2: 0.941 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: model deterimined by MAD phasing

Resolution: 2.8→29.384 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2561	832	4.92 %
R_work	0.2071	-	-
obs	0.2097	16895	97.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→29.384 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3873	0	0	4	3877

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3932
X-RAY DIFFRACTION	f_angle_d	0.846	5328
X-RAY DIFFRACTION	f_dihedral_angle_d	22.542	1407
X-RAY DIFFRACTION	f_chiral_restr	0.054	610
X-RAY DIFFRACTION	f_plane_restr	0.005	694

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 (%)
2.8001-2.9754	0.4064	136	0.3004	2647	X-RAY DIFFRACTION	99
2.9754-3.2048	0.3261	129	0.2601	2649	X-RAY DIFFRACTION	99
3.2048-3.5269	0.2675	140	0.2305	2647	X-RAY DIFFRACTION	99
3.5269-4.0361	0.2653	144	0.1966	2656	X-RAY DIFFRACTION	98
4.0361-5.0808	0.217	135	0.1698	2683	X-RAY DIFFRACTION	97
5.0808-29.384	0.2272	148	0.1992	2781	X-RAY DIFFRACTION	95

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	4.7709	0.1533	-2.2295	3.2712	1.3868	7.6777	0.0071	-0.2682	1.0508	0.4645	0.1511	-0.7023	-0.4841	0.4312	-0.2211	0.3613	0.0325	-0.1399	0.363	-0.0932	1.0598	-7.2993	-3.7779	38.3652
2	3.9642	-0.1671	-2.5406	2.2258	-0.2203	8.1247	0.0475	-0.2432	0.0379	0.1712	0.0636	-0.2769	-0.2028	-0.0555	-0.1286	0.334	-0.0782	-0.1024	0.3679	0.0259	0.8558	-11.6004	-2.2292	41.3405
3	7.7464	-0.9045	1.0113	8.0672	1.4172	4.4928	-0.0378	-0.0922	0.1271	0.5803	0.1065	2.1175	0.1428	-0.2013	-0.1862	0.272	-0.0526	-0.0339	0.415	-0.0622	0.7568	-18.5804	-10.8862	39.3647
4	2.8712	0.0213	-1.4917	4.782	-0.7223	3.9909	0.2257	-0.1147	0.0332	-0.0335	-0.1234	-1.0844	-0.3016	0.5053	-0.0784	0.3862	-0.0192	-0.0402	0.3529	-0.0709	1.1376	-3.691	-7.9748	31.0906
5	6.0039	-0.3121	2.939	1.5205	1.6709	2.2585	0.6523	0.2033	-1.1668	0.0349	0.4853	-0.5671	1.0401	1.4376	-1.0242	0.4593	0.0069	0.0138	0.4135	-0.025	1.1452	5.0903	-14.3253	34.2371
6	5.3587	-0.2975	4.0021	0.7791	1.9004	8.3693	0.2538	-0.0249	-0.2873	0.0321	0.0888	-0.4657	0.3057	0.2769	-0.333	0.4177	0.0082	-0.0366	0.32	-0.0333	0.9767	-3.1726	-16.5751	30.6215
7	2.5428	-1.0262	-1.4739	2.6992	-1.8918	7.8418	0.3906	-0.0094	0.2923	0.2383	0.0408	-0.4916	0.2478	0.037	-0.3855	0.3154	0.0381	-0.0087	0.3192	0.0167	1.2119	-1.214	-16.9829	34.8459
8	7.3834	-1.4298	-2.0532	6.7141	4.9982	7.8412	0.1345	-0.5265	1.6795	-0.1525	0.1432	-0.4255	-1.1331	0.9419	-0.0409	0.4216	-0.0307	0.0079	0.3012	-0.0507	0.9837	-23.462	-2.5489	23.431
9	8.6189	-0.7129	-3.4001	6.9756	-2.069	8.0554	-0.1762	1.2493	1.6739	-1.3868	0.5931	0.4475	0.6841	-0.8533	-0.3904	0.7286	-0.1318	-0.1618	0.6107	0.3907	0.9873	-27.4394	1.1749	8.4321
10	4.5155	-2.0207	0.7235	5.2569	2.2307	1.4191	0.3567	0.9537	1.5126	-1.0346	0.071	-0.9168	-1.2611	0.2153	-0.3796	0.7455	-0.131	0.0269	0.5379	0.2885	0.9133	-20.9516	1.2177	11.4981
11	3.395	0.8792	0.7874	8.334	-0.1512	9.3586	-0.1737	1.2824	0.4872	-1.9471	0.0682	-1.5581	-1.1426	1.0849	0.0314	0.5426	-0.0693	0.2566	0.6258	0.1227	1.3352	-14.3696	-7.2507	11.4379
12	6.4481	2.1827	5.8428	2.7795	4.3888	8.3123	0.3758	0.4566	-0.8759	-0.1596	0.0911	-0.6762	0.2785	0.2547	-0.4044	0.4678	-0.0066	0.0087	0.3057	-0.0662	0.8743	-18.0356	-11.8775	16.1233
13	4.0047	1.3101	2.7712	4.4328	-2.8237	2.3414	-0.7349	-0.0844	0.6253	-0.1344	-0.0604	-0.716	-1.325	-0.3798	0.7329	0.5352	0.0538	-0.0284	0.3602	-0.0435	0.6042	-29.137	-5.8456	18.0889
14	2.1279	-0.3706	4.7118	8.5656	-9.5272	2.1594	-0.5894	-0.7819	0.355	1.1121	0.1051	1.074	-1.0439	-1.774	0.4749	0.6111	0.0813	0.0763	0.5306	-0.1613	0.7377	-37.8829	-3.5937	26.8133
15	7.0044	1.6054	0.4334	4.5238	-1.7743	7.8342	0.4167	-0.1318	-0.125	-0.2863	0.4169	0.8515	-0.3414	-0.5602	-0.8391	0.3269	0.0362	0.0142	0.2022	0.027	0.6648	-37.3594	-12.5472	17.7201
16	8.2647	-0.0629	8.2064	9.1303	-2.4178	2.2124	-0.0171	-0.2476	-1.2737	-0.3208	0.4823	0.3693	0.2677	-0.6869	-0.581	0.3812	-0.1155	0.1336	0.3597	-0.0197	0.5522	-30.1167	-13.9394	20.961
17	4.5439	-0.0421	-0.8807	2.4408	0.8	8.7679	0.3006	-0.2722	-0.8221	0.1785	0.181	-0.6887	1.1503	0.0886	-0.2328	0.4788	0.0231	-0.0451	0.348	0.0639	0.8597	-23.9731	-20.9433	19.5544
18	8.2898	-2.7708	3.9685	3.6313	0.0321	6.2899	-0.1475	-0.1527	0.4065	-0.3155	-0.0124	-0.3404	-0.2744	-0.7693	0.04	0.2627	-0.0079	0.0115	0.3045	0.0679	0.6723	-37.4616	-10.5381	17.9716
19	1.1992	-0.2458	0.8244	2.6948	1.6585	2.3225	-0.4302	0.1564	0.4253	-0.1774	-0.507	-0.0673	0.3904	0.5797	0.9105	1.1177	-0.1336	0.3701	0.6799	0.2714	1.4148	-5.0491	32.262	37.9089
20	5.3549	-0.8063	-2.9373	1.5664	0.1582	2.2539	0.7942	2.0533	1.4436	-1.4671	-0.4861	-0.1241	-1.8523	-0.9537	-0.2895	1.6702	0.2261	0.2481	0.9781	0.354	0.9526	-8.1529	26.7672	25.2355
21	6.3887	3.2013	-2.8101	1.9855	-5.8418	7.119	-0.1759	0.2161	-0.4036	-1.5675	-0.775	-2.3365	0.1722	1.0935	0.9497	0.8325	-0.113	0.3633	0.7171	-0.0847	0.9184	-0.6831	17.9133	30.5598
22	6.4882	2.2801	1.9786	2.0624	9.18	2.11	-0.6545	0.4537	0.4613	-1.2074	-0.2208	0.8218	-0.84	-0.1946	0.8802	0.5347	-0.0046	0.0611	0.4045	0.1493	0.9519	-3.758	18.5183	37.3246
23	2.8228	0.8459	-1.1358	2.9643	-1.7005	5.7941	-0.0015	0.1393	1.3593	-0.3759	0.1595	0.1822	-1.7997	-1.0918	-0.0618	1.1908	0.2925	0.029	0.5437	0.1018	1.3423	-15.3652	30.9766	41.4633
24	8.3869	-2.8289	9.655	2.0565	-4.8754	2.0224	1.7265	0.6543	0.7568	-1.332	-0.292	1.6867	0.7361	-1.8973	-1.4262	0.8267	0.0501	-0.1598	1.0881	0.1798	1.0178	-26.2578	20.7308	35.3783
25	4.9424	-0.5427	-2.5644	4.4929	0.5103	6.6036	0.3334	0.1357	0.0579	0.5211	-0.2645	0.1052	-0.3924	-0.1318	-0.0703	0.5273	-0.0333	0.0195	0.3472	0.0761	1.0163	-10.2273	18.7369	45.9962
26	4.418	1.0405	-6.459	6.6311	1.5579	2.0252	0.8639	0.3989	0.3545	0.0915	0.8078	0.6331	-1.4841	-2.1903	-1.644	0.7928	0.1279	-0.0619	0.5523	0.1118	1.2618	-20.8709	27.8101	42.3035

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 50 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 62 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 63 through 103 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 104 through 123 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 124 through 143 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 144 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 11 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 12 through 26 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 27 through 50 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 51 through 62 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 63 through 73 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 74 through 89 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 90 through 103 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 104 through 127 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 128 through 137 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 138 through 157 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 158 through 169 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid -1 through 11 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 12 through 50 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 51 through 62 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 63 through 73 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 74 through 113 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 114 through 130 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 131 through 157 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 158 through 168 )

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