PDB-22ap: Crystal structure of Bacillus cereus GmaR in complex with UDP-Glc...

ID or keywords:

Entry

Database: PDB / ID: 22ap

Title

Crystal structure of Bacillus cereus GmaR in complex with UDP-GlcNAc and Mg2+

Components

GmaR

Keywords

TRANSFERASE / glycosyltransferase

Function / homology

URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Function and homology information

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.42 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	22ap.cif.gz	150.2 KB	Display	PDBx/mmCIF format
PDB format	pdb22ap.ent.gz	116.9 KB	Display	PDB format
PDBx/mmJSON format	22ap.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/22ap ftp://data.pdbj.org/pub/pdb/validation_reports/2a/22ap	HTTPS FTP

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Related structure data

Related structure data	22aoSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: GmaR

B: GmaR

hetero molecules

47.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GmaR

hetero molecules

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

2

B: GmaR

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.946, 78.946, 215.085
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	GmaR Mass: 23147.973 Da / Num. of mol.: 2 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: Chemical	ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₇N₃O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.09 Å³/Da / Density % sol: 41.14 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: PEG 3350, magnesium chloride, calcium acetate, MES

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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: 2.42→30 Å / Num. obs: 15942 / % possible obs: 98.4 % / Redundancy: 6.9 % / CC_1/2: 0.998 / Net I/σ(I): 40.6
Reflection shell	Resolution: 2.42→2.46 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 781 / CC_1/2: 0.88 / % possible all: 99

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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: 22AO

22ao

Resolution: 2.42→29.084 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2437	843	5.35 %
R_work	0.2003	-	-
obs	0.2026	15755	98.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.42→29.084 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2544	0	80	9	2633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2665
X-RAY DIFFRACTION	f_angle_d	0.909	3625
X-RAY DIFFRACTION	f_dihedral_angle_d	14.344	1603
X-RAY DIFFRACTION	f_chiral_restr	0.055	425
X-RAY DIFFRACTION	f_plane_restr	0.005	458

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 (%)
2.4201-2.5717	0.2959	142	0.2541	2413	X-RAY DIFFRACTION	99
2.5717-2.7701	0.3414	139	0.2452	2419	X-RAY DIFFRACTION	99
2.7701-3.0486	0.3333	138	0.2441	2457	X-RAY DIFFRACTION	99
3.0486-3.4891	0.3102	135	0.214	2472	X-RAY DIFFRACTION	99
3.4891-4.3934	0.1958	140	0.1685	2521	X-RAY DIFFRACTION	99
4.3934-29.084	0.205	149	0.1866	2630	X-RAY DIFFRACTION	97

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	9.6818	-6.89	7.1191	4.8754	-4.9479	5.1137	0.5381	0.6244	0.9781	-1.3066	-0.4794	0.5113	0.7223	-0.6953	-0.6923	0.762	-0.0316	-0.22	0.7368	0.1562	0.9419	-20.9052	-22.046	-14.4443
2	7.2256	0.7567	-2.9656	7.2781	-2.6911	2.2742	-0.3541	-0.2782	-0.4402	0.5882	0.0962	0.2006	0.3842	-0.1237	0.2765	0.3598	0.0413	-0.0523	0.4364	-0.0341	0.3486	-4.6608	-29.1663	0.8782
3	7.2499	5.3585	-5.9271	4.5987	-4.6721	4.9858	-0.5522	0.6874	-0.6099	-0.7952	0.1382	0.2001	1.1742	-0.6272	0.2551	0.389	0.0454	-0.0539	0.4947	-0.0649	0.4834	-6.3841	-33.9855	-6.0379
4	7.51	-1.5132	0.9952	9.3845	-5.153	3.1588	-0.1984	0.242	0.8273	-0.5773	0.291	0.5461	0.4977	-0.7587	0.1767	0.3417	0.0313	-0.0369	0.3618	-0.1382	0.4742	-18.7857	-22.3697	-5.2197
5	6.3988	1.5438	-0.6963	6.694	-1.2726	5.9043	-0.029	-1.6274	0.647	0.4909	0.0663	-0.1437	-0.2745	-0.4921	-0.1282	0.346	0.0471	0.0605	0.6848	-0.2057	0.3781	11.0825	-20.1295	17.0946
6	2.8318	-0.7359	0.0894	5.3851	3.6297	3.5892	0.4558	-2.5825	1.0073	0.6253	-0.3454	-0.0284	-0.2482	-0.2064	-0.2406	0.4776	0.0407	-0.0129	1.1347	-0.2661	0.4823	5.9376	-19.5868	20.1538
7	5.7693	-1.673	-1.7287	4.7458	2.0773	3.6571	0.0476	-1.7001	0.183	-0.3829	-0.4561	1.7074	0.0702	-0.6297	0.3452	0.242	0.0452	0.0644	0.9788	-0.1535	0.5797	-0.7519	-27.0456	16.8484
8	6.1327	2.2477	1.5734	3.513	1.4434	1.9625	-0.0761	-0.8223	0.3945	-0.1211	-0.2226	0.0862	-0.1902	-0.2768	0.2672	0.3319	0.0832	0.0006	0.4469	-0.0341	0.2869	9.6832	-25.9878	11.6048
9	7.7109	2.6394	-2.4594	7.1121	1.9519	5.9387	-0.1557	-0.0023	0.5638	-0.9753	0.0848	0.0794	-0.4672	0.0234	0.0609	0.2959	-0.0262	-0.0209	0.3489	-0.0238	0.2541	21.7068	-22.9309	3.4146
10	5.6784	-1.8984	5.7511	2.2788	-2.4785	5.9872	0.7075	-0.913	-0.3311	0.1466	-0.555	-0.4057	1.6269	0.5906	-0.1413	0.6391	0.0979	0.0078	0.6078	0.0915	0.516	23.8396	-34.1979	17.4358
11	7.8764	-0.7223	2.9505	8.1617	0.4479	6.8067	-0.3012	0.0888	-0.1063	-0.4772	-0.0387	0.3619	-0.1524	0.022	0.4038	0.2693	-0.0159	0.0111	0.3196	0.0363	0.2324	10.0264	-29.8528	3.5153
12	6.6374	2.631	-6.5588	8.9303	-3.164	7.074	-0.5073	0.0369	-0.7573	-0.1151	0.5216	0.5093	0.9319	0.1456	-0.3162	0.3646	-0.1134	0.0667	0.5294	0.0671	0.4996	9.6323	-37.872	4.6825
13	8.3819	0.5449	-0.8526	7.4176	1.9399	2.3035	-0.1471	-0.4359	0.2834	0.0322	0.4967	-0.6412	-0.3717	0.9553	-0.2835	0.2226	-0.0079	0.0108	0.2894	-0.037	0.275	22.3923	-28.3883	10.6646
14	4.6923	0.5992	-0.8857	5.4426	-0.8247	3.5366	-0.217	0.7511	2.4382	-0.6705	-0.2231	0.5329	-0.7315	-0.1105	0.1809	0.6935	-0.0206	-0.2709	0.4581	0.2772	1.3024	-4.7401	-11.4736	-6.8493
15	5.6081	1.1498	0.9177	7.5666	3.0784	7.5768	-0.5845	1.2957	1.2729	-0.5805	0.9491	-0.5448	-0.6687	0.7868	-0.5125	0.52	-0.214	-0.0713	0.6008	0.2314	0.9654	4.4214	-18.5468	-9.6928
16	8.1899	-0.9853	1.1552	3.0273	-0.3408	3.2315	-0.3045	0.3481	1.4779	-0.0689	-0.0005	-0.1315	-0.5901	-0.2873	0.271	0.4179	0.0056	-0.136	0.4144	0.0099	0.5605	-5.9689	-20.3557	-4.7018
17	6.9812	-2.9909	3.0379	5.3736	-4.3617	5.0095	-0.3539	-1.7563	1.6371	0.9533	0.3952	0.7121	-0.9865	-1.4756	-0.3668	0.5114	0.1226	-0.0783	0.6824	-0.2147	0.8455	-19.3911	-17.3084	4.8395
18	2.8979	0.5963	-2.0751	7.7826	-0.9556	3.3099	-0.0247	-0.3889	0.0984	0.558	-0.0262	0.0419	0.1394	-0.1556	0.1729	0.2483	0.0078	-0.0247	0.5925	-0.037	0.5056	-16.4362	-27.8118	3.4262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 114 through 133 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 134 through 143 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 144 through 157 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 158 through 169 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1 through 26 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 27 through 50 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 51 through 62 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 63 through 89 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 90 through 113 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 114 through 130 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 131 through 143 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 144 through 157 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 158 through 169 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 1 through 50 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 51 through 62 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 63 through 89 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 90 through 103 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 104 through 113 )

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