PDB-9j1u: Structural basis of the bifunctionality of M. salinexigens ZYF650...

ID or keywords:

Entry

Database: PDB / ID: 9j1u

Title

Structural basis of the bifunctionality of M. salinexigens ZYF650T glucosylglycerol phosphorylase in glucosylglycerol catabolism

Components

Sucrose phosphorylase

Keywords

STRUCTURAL PROTEIN / Glucosylglycerol / phosphorylase-GH13_18 / structure-double displacement mechanism

Function / homology

Function and homology information

sucrose phosphorylase / sucrose phosphorylase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Marinobacter salinexigens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.72 Å

Authors

Lu, D. / Ma, H.L.

Funding support

China, 1items

Citation

Journal: J Biol Chem / Year: 2025
Title: Structural basis of the bifunctionality of Marinobacter salinexigens ZYF650 glucosylglycerol phosphorylase in glucosylglycerol catabolism.
Authors: Di Lu / Keke Zhang / Chen Cheng / Danni Wu / Lei Yin / Quan Luo / Meiyun Shi / Honglei Ma / Xuefeng Lu /

Abstract: 2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and ...

History

Deposition	Aug 5, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9j1u.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9j1u.ent.gz	972.5 KB	Display	PDB format
PDBx/mmJSON format	9j1u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9j1u_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	9j1u_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9j1u_validation.xml.gz	115.5 KB	Display
Data in CIF	9j1u_validation.cif.gz	146 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j1/9j1u ftp://data.pdbj.org/pub/pdb/validation_reports/j1/9j1u	HTTPS FTP

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Related structure data

Related structure data	61086C 9j22C 9j24C 9j25C 7xdqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#74 - Feb 2006 alpha-Amylase similarity (3) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #138 - Jun 2011 Glucansucrase similarity (3) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1)

Deposited unit

F: Sucrose phosphorylase

B: Sucrose phosphorylase

C: Sucrose phosphorylase

D: Sucrose phosphorylase

E: Sucrose phosphorylase

A: Sucrose phosphorylase

hetero molecules

331 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	111.830, 178.500, 180.240
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 6 molecules FBCDEA

#1: Protein	Sucrose phosphorylase / Glucosylglycerol phosphorylase Mass: 54903.852 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinobacter salinexigens (bacteria) / Gene: gtfA, FWJ25_14990 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B0VBK8, sucrose phosphorylase

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Sugars , 2 types, 4 molecules

#2: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#5: Sugar

ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose

Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃O₉P / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 145 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.73 Å³/Da / Density % sol: 54.95 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion Details: 0.1 M Sodium chloride, 0.1 M BIS-TRIS propane pH 9.0, 25% Polyethylene glycol 1,500

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.72→31.11 Å / Num. obs: 96759 / % possible obs: 99.3 % / Redundancy: 5.7 % / R_merge(I) obs: 0.074 / R_pim(I) all: 0.051 / R_rim(I) all: 0.096 / Net I/σ(I): 14.7
Reflection shell	Resolution: 2.72→2.79 Å / R_merge(I) obs: 0.747 / Num. unique obs: 6676 / R_pim(I) all: 0.626 / R_rim(I) all: 0.98

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
HKL-3000	7.21	data reduction
HKL-3000	7.21	data scaling
PHASER	2.7.0	phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XDQ

7xdq

Resolution: 2.72→21.04 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2539	4609	4.78 %	RANDOM
R_work	0.2144	-	-	-
obs	0.2163	96434	99.27 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.72→21.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23130	0	107	134	23371

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	23803
X-RAY DIFFRACTION	f_angle_d	1.027	32343
X-RAY DIFFRACTION	f_dihedral_angle_d	17.733	3192
X-RAY DIFFRACTION	f_chiral_restr	0.055	3530
X-RAY DIFFRACTION	f_plane_restr	0.007	4218

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 (%)
2.72-2.75	0.4489	149	0.397	2811	X-RAY DIFFRACTION	92
2.75-2.78	0.4214	121	0.3797	2889	X-RAY DIFFRACTION	95
2.78-2.82	0.4192	150	0.3743	2993	X-RAY DIFFRACTION	98
2.82-2.85	0.4292	138	0.3549	3032	X-RAY DIFFRACTION	100
2.85-2.89	0.3914	181	0.3418	3018	X-RAY DIFFRACTION	100
2.89-2.93	0.3461	164	0.3309	3028	X-RAY DIFFRACTION	100
2.93-2.97	0.3126	147	0.3219	3055	X-RAY DIFFRACTION	100
2.97-3.02	0.3289	149	0.3191	3099	X-RAY DIFFRACTION	100
3.02-3.06	0.332	162	0.2983	2971	X-RAY DIFFRACTION	100
3.06-3.11	0.302	191	0.2991	3048	X-RAY DIFFRACTION	100
3.11-3.17	0.3845	148	0.3036	3057	X-RAY DIFFRACTION	100
3.17-3.22	0.3608	123	0.2799	3090	X-RAY DIFFRACTION	100
3.22-3.29	0.3177	140	0.2822	3076	X-RAY DIFFRACTION	100
3.29-3.35	0.2868	157	0.2501	3040	X-RAY DIFFRACTION	100
3.35-3.42	0.2677	162	0.2425	3068	X-RAY DIFFRACTION	100
3.42-3.5	0.301	171	0.2434	3047	X-RAY DIFFRACTION	100
3.5-3.59	0.2426	144	0.2331	3079	X-RAY DIFFRACTION	100
3.59-3.69	0.3163	158	0.2382	3051	X-RAY DIFFRACTION	100
3.69-3.8	0.2671	153	0.2247	3096	X-RAY DIFFRACTION	100
3.8-3.92	0.2181	129	0.2063	3093	X-RAY DIFFRACTION	100
3.92-4.06	0.238	157	0.2022	3077	X-RAY DIFFRACTION	100
4.06-4.22	0.2162	122	0.1843	3101	X-RAY DIFFRACTION	100
4.22-4.41	0.2065	160	0.1651	3095	X-RAY DIFFRACTION	100
4.41-4.64	0.2247	145	0.1688	3109	X-RAY DIFFRACTION	100
4.64-4.92	0.248	160	0.1658	3092	X-RAY DIFFRACTION	100
4.92-5.3	0.1889	167	0.1574	3112	X-RAY DIFFRACTION	100
5.3-5.82	0.2232	156	0.1762	3119	X-RAY DIFFRACTION	100
5.82-6.64	0.2254	169	0.1713	3136	X-RAY DIFFRACTION	100
6.64-8.28	0.2088	175	0.1794	3151	X-RAY DIFFRACTION	100
8.28-21.04	0.1761	161	0.1612	3192	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	1.7656	0.4367	-0.6597	0.8323	-0.623	2.5152	-0.0215	-0.3461	-0.3444	0.1112	-0.0059	-0.0812	0.5274	0.4804	0.0242	0.8379	0.1841	-0.0237	0.4204	-0.0002	0.5281	-21.2252	-2.2383	-15.4109
2	1.624	0.9557	-0.9484	2.3419	-0.4829	2.009	0.0387	-0.153	-0.1135	0.2489	-0.0325	-0.3419	0.3137	0.6881	-0.066	0.5547	0.1547	-0.0353	0.6083	-0.0136	0.4768	-8.2229	4.9676	-24.57
3	1.2779	0.6542	0.1793	0.366	-0.1351	1.5852	0.003	0.276	-0.0279	0.2033	-0.1465	-0.0197	0.5883	0.163	0.1005	0.4307	0.08	-0.0136	0.371	0.0098	0.5044	-26.4877	3.5239	-36.287
4	1.5709	0.4543	-0.1792	1.7216	-0.9727	2.172	0.1011	-0.1692	0.1382	0.1835	-0.0236	-0.2361	-0.0874	0.194	-0.1017	0.373	-0.0052	-0.0374	0.3587	-0.0381	0.5262	-33.7472	14.6208	-24.2987
5	0.1508	-0.1958	-0.3799	0.5014	1.1551	5.8346	-0.2101	0.3645	0.1715	0.2611	0.0224	0.4902	1.4005	-0.669	-0.0272	0.378	-0.1683	0.0039	0.6173	0.0143	0.7055	-50.1558	1.6391	-35.4536
6	2.222	0.7336	-0.0351	0.3528	0.2968	2.1482	-0.1529	0.3171	-0.2538	-0.1555	0.1781	0.0636	0.496	0.1754	-0.0241	0.8139	0.0801	0.0321	0.334	-0.0278	0.547	-26.2358	-1.398	-77.7723
7	1.6213	-0.8519	-0.8742	2.1705	0.9862	2.8137	0.0129	0.2663	-0.1948	-0.1944	-0.1783	0.1556	0.2868	-0.7053	0.0608	0.62	-0.1378	-0.0531	0.5379	-0.0454	0.4955	-51.4572	5.5385	-71.4931
8	2.0536	-0.28	-0.3089	0.0958	-0.0922	1.5878	0.1788	-0.1576	-0.1733	-0.1378	-0.169	0.1284	0.6292	-0.014	0.032	0.5859	0.0093	0.0148	0.3072	-0.01	0.4516	-32.7914	4.1766	-57.1642
9	2.1294	0.1195	-0.5906	1.6519	0.3067	2.6231	0.0722	-0.1551	0.0735	-0.3082	-0.0295	-0.099	0.3396	0.5384	-0.0335	0.3877	0.0935	0.0164	0.4568	-0.0139	0.4704	-16.2188	10.8347	-63.246
10	0.7	-0.2724	-0.0229	2.0351	-0.5713	1.1491	0.0447	0.2243	0.0001	-0.5082	-0.0594	-0.654	-0.2226	0.7862	0.056	0.8535	-0.5032	0.1855	1.4284	-0.1495	0.774	14.7785	42.8517	-65.4519
11	1.1691	1.1251	-0.4928	2.2026	-0.7025	2.2093	-0.2722	0.3172	-0.7283	-0.621	0.2099	0.0178	0.1342	0.1665	0.2673	0.4232	-0.001	0.0283	1.3674	-0.1763	1.0038	5.6953	19.5564	-55.936
12	0.7931	-0.4597	-0.326	0.6108	-0.1621	1.2307	-0.1138	-0.0211	-0.4298	-0.5059	0.3335	-0.6185	-0.043	1.0095	0.1485	0.628	-0.315	0.1745	1.5807	-0.1583	0.8325	14.3035	33.512	-54.5773
13	2.0946	0.2736	-0.7554	1.5231	-0.2903	0.3182	-0.0364	-0.2177	-0.2969	0.0339	0.1198	-0.1843	-0.4009	0.8174	-0.0935	0.6382	-0.4138	0.0419	1.1154	-0.0986	0.6881	3.4609	47.5636	-46.8832
14	2.6737	0.5265	-0.3562	1.9659	-0.6246	0.2107	-0.1683	0.1683	-0.3091	-0.1994	0.0658	-0.0272	-0.493	0.4933	-0.064	0.8661	-0.4431	0.0223	0.7528	-0.007	0.6614	-8.5038	46.5844	-52.6324
15	2.3579	0.967	-0.068	3.1466	-0.4038	1.0076	0.0549	0.1207	-0.3704	-0.1839	0.0957	0.3525	-0.7137	0.477	-0.0984	0.9659	-0.3311	0.0584	0.7531	-0.0791	0.708	-10.4402	46.6752	-58.99
16	1.5018	0.5642	-0.2526	1.7244	-0.3116	0.081	-0.0267	0.2072	0.1328	-0.1825	0.0984	0.0959	-0.5893	0.5256	-0.0515	1.2013	-0.6231	0.1203	0.9082	-0.072	0.619	-2.6595	58.0064	-61.7995
17	1.8606	0.694	0.0784	2.1668	-0.3638	0.084	-0.1562	0.2476	0.7559	0.019	-0.042	0.2918	-0.6144	0.4125	-0.0176	1.6289	-0.5663	0.1123	0.8735	0.0366	0.8337	-6.0008	73.14	-52.275
18	0.311	0.1828	-0.2315	0.4993	0.6098	1.783	0.0168	-0.2373	-0.1344	-0.181	-0.3326	0.454	-0.3809	-0.8688	0.2344	0.5089	0.2972	0.0245	1.129	-0.0324	0.8357	-70.2902	41.606	-23.7802
19	1.5456	-0.9567	-0.9851	1.1586	0.5457	3.773	-0.1366	-0.1355	-0.3273	0.2262	-0.0377	0.2664	0.1157	-0.2196	0.0899	0.542	0.0313	0.0532	0.7108	0.0152	0.74	-61.5025	19.1207	-34.9496
20	0.7083	0.1422	-0.2335	1.7923	0.3905	1.3695	-0.1412	-0.0324	-0.0372	-0.2056	0.0043	0.3016	-0.2676	-0.703	0.0801	0.5458	0.2822	-0.0124	0.7755	-0.0089	0.5407	-64.3016	40.7567	-38.9449
21	3.3063	0.4628	-1.0429	2.5192	1.1288	3.59	0.0585	-0.1256	-0.2103	-0.1473	-0.004	0.0182	-0.2111	-0.121	0.0946	0.5313	0.1312	0.012	0.4727	-0.0712	0.5856	-47.1809	46.1419	-36.7066
22	1.2712	0.329	-0.7326	0.9947	0.7057	1.6806	0.0825	-0.2657	-0.087	-0.3017	-0.003	-0.1752	-0.5335	-0.142	-0.1096	0.6826	0.2517	0.0002	0.5067	0.0486	0.566	-49.7843	50.1775	-24.4687
23	2.8792	-0.0435	0.2154	2.8865	0.4263	0.5371	-0.0579	-0.1141	0.576	-0.4046	0.0895	-0.1327	-1.1797	-0.4587	-0.1041	1.5597	0.3435	0.0137	0.6168	0.002	0.6938	-50.9741	70.0582	-38.6429
24	0.7003	-0.4698	0.2713	1.8355	-0.1454	1.6438	-0.0491	-0.2677	0.3078	0.5616	-0.0026	-0.0464	-0.7945	0.484	0.0538	1.0062	-0.5972	0.0832	0.9538	-0.1458	0.7256	-4.1968	61.2741	-8.2868
25	1.1008	0.0638	0.531	0.9673	1.6804	3.0657	0.1205	-0.1745	0.4284	0.0868	-0.1212	0.2036	-0.7953	-0.3561	0.151	1.2972	-0.2561	0.1382	0.767	-0.1389	0.8465	-24.9499	69.9622	-22.2803
26	0.2241	0.0217	0.5256	0.58	0.4843	1.911	-0.0064	0.0328	0.1763	-0.1466	0.0232	-0.1314	-1.6458	0.4938	-0.0794	0.9169	-0.7393	0.1464	0.9384	-0.0883	0.8221	-5.1754	59.8743	-24.5424
27	0.6163	0.2606	-0.0036	1.2891	-0.0602	1.2099	0.0487	0.0342	-0.0333	0.0826	-0.0463	-0.0715	-0.1837	0.5035	-0.0233	0.4428	-0.2778	0.0244	0.9609	-0.0412	0.6906	-4.2351	38.9184	-19.5476
28	0.5868	-0.1504	0.1355	1.5656	-0.6416	0.7624	0.0724	0.2114	0.276	-0.6504	-0.1197	-0.0229	-0.9133	-0.2442	0.0526	1.6243	0.4308	0.0909	0.6939	0.0547	0.6824	-49.169	63.2587	-70.6725
29	1.5538	0.2689	0.2433	3.9443	0.8609	3.8267	0.2345	0.2048	-0.0209	-0.913	-0.1832	-0.3993	-0.6276	0.1898	-0.0586	0.8558	0.1675	0.1276	0.4483	0.0388	0.5024	-42.8528	44.5229	-66.1818
30	1.131	0.5633	-0.0287	2.594	-0.0318	2.2765	0.0668	0.2868	-0.1202	-0.6578	-0.1891	0.1475	-0.3236	-0.6603	0.041	0.8654	0.3532	-0.046	0.6631	-0.0606	0.5532	-57.8599	37.9907	-72.8333

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 2 through 117 )
2	X-RAY DIFFRACTION	2	chain 'F' and (resid 118 through 208 )
3	X-RAY DIFFRACTION	3	chain 'F' and (resid 209 through 276 )
4	X-RAY DIFFRACTION	4	chain 'F' and (resid 277 through 408 )
5	X-RAY DIFFRACTION	5	chain 'F' and (resid 409 through 480 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 83 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 84 through 182 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 183 through 276 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 277 through 480 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 117 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 118 through 146 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 147 through 208 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 209 through 276 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 277 through 315 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 316 through 361 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 362 through 447 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 448 through 480 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 2 through 117 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 118 through 146 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 147 through 276 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 277 through 315 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 316 through 423 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 424 through 480 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 2 through 117 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 118 through 146 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 147 through 276 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 277 through 480 )
28	X-RAY DIFFRACTION	28	chain 'A' and (resid 2 through 276 )
29	X-RAY DIFFRACTION	29	chain 'A' and (resid 277 through 361 )
30	X-RAY DIFFRACTION	30	chain 'A' and (resid 362 through 480 )

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