PDB-9j24: Structural basis of the bifunctionality of M. salinexigens ZYF650...

ID or keywords:

Entry

Database: PDB / ID: 9j24

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: 2.5 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 6, 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	9j24.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9j24.ent.gz	981.8 KB	Display	PDB format
PDBx/mmJSON format	9j24.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9j24_validation.pdf.gz	8.4 MB	Display	wwPDB validaton report
Full document	9j24_full_validation.pdf.gz	8.4 MB	Display
Data in XML	9j24_validation.xml.gz	131.1 KB	Display
Data in CIF	9j24_validation.cif.gz	173 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j2/9j24 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/9j24	HTTPS FTP

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Related structure data

Related structure data	61086C 9j1uC 9j22C 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

B: Sucrose phosphorylase

D: Sucrose phosphorylase

C: Sucrose phosphorylase

A: Sucrose phosphorylase

E: Sucrose phosphorylase

F: Sucrose phosphorylase

hetero molecules

333 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)	172.727, 115.065, 182.134
Angle α, β, γ (deg.)	90.00, 100.56, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-827- HOH

#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

#2: Chemical

...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION

#3: Sugar

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

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#4: Chemical

ChemComp-PEG / DI(HYDROXYETHYL)ETHER

Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1227 / 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: 2.7 Å³/Da / Density % sol: 54.45 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / Details: 8% PEG 6000, 1.6 M Sodium chloride, 20% Glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.29→54.8 Å / Num. obs: 157587 / % possible obs: 99.9 % / Redundancy: 6.8 % / R_merge(I) obs: 0.128 / R_pim(I) all: 0.081 / R_rim(I) all: 0.152 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.29→2.35 Å / Num. unique obs: 11662 / R_pim(I) all: 0.822

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XDQ

7xdq

Resolution: 2.5→48.39 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2115	5919	4.93 %
R_work	0.1743	-	-
obs	0.1761	120051	99.06 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→48.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23124	0	241	1227	24592

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	23919
X-RAY DIFFRACTION	f_angle_d	1.262	32461
X-RAY DIFFRACTION	f_dihedral_angle_d	14.782	3260
X-RAY DIFFRACTION	f_chiral_restr	0.068	3540
X-RAY DIFFRACTION	f_plane_restr	0.009	4217

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 (%)
2.5-2.53	0.2937	196	0.2412	3613	X-RAY DIFFRACTION	94
2.53-2.56	0.291	175	0.2401	3667	X-RAY DIFFRACTION	97
2.56-2.59	0.3104	196	0.2418	3728	X-RAY DIFFRACTION	97
2.59-2.62	0.2599	175	0.2299	3809	X-RAY DIFFRACTION	99
2.62-2.66	0.2614	212	0.2207	3803	X-RAY DIFFRACTION	100
2.66-2.69	0.2598	207	0.214	3761	X-RAY DIFFRACTION	100
2.69-2.73	0.2797	227	0.2153	3845	X-RAY DIFFRACTION	100
2.73-2.77	0.2652	199	0.227	3766	X-RAY DIFFRACTION	100
2.77-2.82	0.2736	195	0.2276	3848	X-RAY DIFFRACTION	100
2.82-2.86	0.3018	194	0.2203	3808	X-RAY DIFFRACTION	100
2.86-2.91	0.2915	193	0.2225	3838	X-RAY DIFFRACTION	100
2.91-2.96	0.2588	206	0.2183	3881	X-RAY DIFFRACTION	100
2.96-3.02	0.2683	196	0.2171	3769	X-RAY DIFFRACTION	100
3.02-3.08	0.2571	228	0.2075	3803	X-RAY DIFFRACTION	100
3.08-3.15	0.2298	206	0.2009	3850	X-RAY DIFFRACTION	100
3.15-3.22	0.2223	194	0.1978	3806	X-RAY DIFFRACTION	100
3.22-3.3	0.2347	181	0.1951	3843	X-RAY DIFFRACTION	100
3.3-3.39	0.2044	172	0.1893	3866	X-RAY DIFFRACTION	100
3.39-3.49	0.2139	211	0.1737	3828	X-RAY DIFFRACTION	100
3.49-3.61	0.2139	197	0.1722	3797	X-RAY DIFFRACTION	100
3.61-3.73	0.2212	189	0.1632	3857	X-RAY DIFFRACTION	100
3.73-3.88	0.173	212	0.1509	3789	X-RAY DIFFRACTION	100
3.88-4.06	0.1737	216	0.1391	3841	X-RAY DIFFRACTION	100
4.06-4.27	0.1771	188	0.1355	3835	X-RAY DIFFRACTION	100
4.27-4.54	0.1558	204	0.1291	3839	X-RAY DIFFRACTION	99
4.54-4.89	0.1837	184	0.129	3832	X-RAY DIFFRACTION	99
4.89-5.38	0.1522	200	0.1363	3807	X-RAY DIFFRACTION	99
5.38-6.16	0.1904	218	0.1558	3816	X-RAY DIFFRACTION	99
6.16-7.76	0.1799	173	0.165	3840	X-RAY DIFFRACTION	98
7.76-48.39	0.173	175	0.155	3747	X-RAY DIFFRACTION	94

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	0.9655	-0.3008	0.1598	3.3933	0.0296	1.221	-0.0144	-0.2624	0.0157	0.4701	0.0298	-0.274	0.0247	0.1454	-0.0347	0.2428	-0.0092	-0.0458	0.3883	-0.0034	0.2371	-15.2779	-57.4558	75.4342
2	1.6171	-0.2609	0.7182	1.6436	-0.1869	1.5847	-0.1095	-0.0897	0.3531	0.104	-0.02	-0.1581	-0.3127	0.1151	0.0985	0.2805	-0.0664	-0.0423	0.2765	-0.0274	0.3501	-21.3917	-39.1353	65.3356
3	2.2585	-0.1269	0.5171	1.2998	0.1868	1.3915	0.0146	-0.1659	0.0567	0.1376	-0.0303	0.0586	0.0024	0.0065	0.0189	0.2046	0.0196	0.0048	0.2215	-0.0107	0.2243	-30.4559	-65.3893	62.7038
4	3.7749	-0.7571	0.0414	2.2883	-0.1319	1.5798	0.1077	0.2028	-0.5399	-0.0169	-0.0314	-0.2206	0.1669	0.249	-0.0583	0.3326	0.1027	-0.003	0.3089	-0.0593	0.3788	-17.4051	-78.7673	50.3169
5	1.6067	-0.5376	0.1529	1.2127	0.4976	1.882	0.047	0.5298	-0.1175	-0.1413	-0.2568	0.2521	-0.0553	-0.52	0.1301	0.3045	0.0146	-0.0651	0.5388	-0.0217	0.2663	-81.2433	-76.4683	10.7396
6	1.3739	0.017	-0.5039	0.6991	1.0314	2.3632	0.0103	0.1861	0.093	-0.048	-0.1935	0.2609	-0.0138	-0.5851	0.1148	0.2495	0.0059	-0.0564	0.3891	-0.0205	0.2871	-87.1585	-71.3285	25.5382
7	2.7228	0.0249	0.923	0.8702	0.4403	1.0718	0.0125	0.1603	0.0239	-0.1078	0.0169	0.0937	0.164	0.0013	-0.0714	0.2927	0.038	-0.0161	0.2488	0.0048	0.2495	-64.9586	-79.8581	30.1044
8	5.144	2.5774	1.4689	3.2115	1.2766	3.2854	0.0061	0.0844	0.2392	0.0314	-0.0576	0.2729	0.0869	-0.0749	0.0659	0.2696	0.0842	0.0225	0.2618	-0.0003	0.2504	-61.7254	-72.426	28.3518
9	2.0018	0.2182	0.342	1.4691	0.7865	1.6983	-0.0354	0.5031	0.3108	-0.2436	0.1026	-0.0832	-0.1276	0.1923	-0.0666	0.2528	0.0226	0.0051	0.3937	0.056	0.2816	-59.5984	-72.1732	14.7568
10	2.2627	0.3549	-0.8578	3.5718	-0.3235	2.0118	0.0767	0.1952	-0.6132	0.0082	0.1255	-0.5572	0.5504	0.2807	-0.1902	0.4121	0.144	-0.0491	0.3269	-0.0799	0.4522	-49.6465	-93.0616	23.0845
11	0.9111	-0.431	0.2389	1.4305	-0.2337	1.3002	-0.0172	-0.5277	-0.8379	0.223	-0.0648	-0.0859	0.508	0.1308	-0.0094	0.6778	0.0529	-0.0501	0.4114	0.2361	0.6013	-56.8353	-101.8377	63.2821
12	1.0797	0.0235	-0.4793	1.0748	-0.2472	1.3708	0.0871	-0.2114	-0.5074	0.0326	-0.0197	-0.1326	0.4171	0.2027	-0.0297	0.4886	0.0899	-0.079	0.2485	0.0435	0.4881	-49.5478	-97.2728	49.5356
13	1.7757	-0.2778	0.1295	1.4632	0.1126	0.6215	0.002	-0.3785	-0.1354	0.1875	0.0062	-0.0887	0.1997	-0.0168	-0.0075	0.3038	-0.0145	-0.0195	0.2683	0.0605	0.2434	-65.2525	-79.6249	60.1602
14	4.0097	1.7053	-0.2254	6.068	0.2043	2.9344	0.0729	-0.0825	-0.0693	0.1193	-0.064	0.659	0.3911	-0.4123	-0.087	0.2772	-0.0444	-0.0197	0.3239	0.037	0.2832	-86.0381	-80.8986	52.0076
15	1.2686	-0.0011	-0.2881	0.7975	0.1185	1.6006	-0.0277	-0.7667	0.3002	0.4138	-0.1288	0.2522	0.0473	-0.4559	0.1065	0.4113	0.1031	0.0774	0.6939	-0.152	0.3957	-82.0109	-42.8006	79.6513
16	0.7455	-0.9501	-0.4439	1.7875	1.8286	3.4023	-0.0611	-0.408	0.0123	0.2013	-0.0202	0.204	0.2414	-0.4775	-0.0167	0.3014	-0.0049	0.078	0.5292	-0.0605	0.3698	-89.266	-53.9001	66.8489
17	0.8739	0.3731	-0.0505	0.9461	0.01	0.4043	-0.057	-0.173	0.2776	0.0272	0.0131	0.1605	-0.1625	-0.1886	-0.0161	0.3182	0.0987	-0.0013	0.3294	-0.0905	0.3356	-75.4477	-38.6662	60.8099
18	4.7165	-0.3626	-1.5743	3.021	0.1625	4.6964	-0.0828	-0.037	-0.1201	0.0574	-0.0383	0.0419	-0.0611	-0.2577	0.113	0.2192	0.016	-0.0228	0.2536	-0.0757	0.2893	-62.9275	-44.2552	61.2334
19	1.8123	0.0372	-0.0962	1.7676	0.6573	1.8033	-0.0791	-0.5408	0.1393	0.2699	0.0473	-0.0991	-0.0338	0.0107	0.0378	0.3041	0.076	-0.0254	0.3848	-0.0892	0.3142	-60.2214	-44.2204	74.6531
20	1.2686	-0.0642	-0.1276	6.0497	1.6011	2.2939	-0.0332	-0.3617	0.7278	-0.1591	0.1355	-0.1773	-0.4887	0.0297	-0.1708	0.4265	0.0152	-0.0555	0.2976	-0.1466	0.5983	-53.4441	-22.2473	66.1004
21	0.3246	0.3328	-0.2219	0.9616	-0.0097	1.3019	-0.3926	0.6081	0.9222	-0.2922	-0.1398	-0.2547	-0.7429	0.0573	-0.3547	0.7412	-0.022	-0.1312	0.3631	0.4012	0.8964	-62.8927	-14.4273	26.2498
22	0.3863	-0.464	0.7956	1.2221	-0.4008	1.7208	-0.2355	0.3331	0.9465	-0.1087	-0.0693	-0.2601	-0.5	0.3743	0.1305	0.5149	-0.0578	-0.0767	0.3258	0.1711	0.8829	-49.515	-17.1982	37.2787
23	0.7172	0.4241	0.183	3.0777	-0.1745	1.1664	-0.0412	0.0218	0.4176	0.0011	-0.0062	-0.2079	-0.2577	-0.0575	0.014	0.3287	0.0788	-0.0331	0.2358	-0.0101	0.4601	-66.4475	-31.6343	41.1964
24	2.4619	-0.0495	0.2085	1.2524	0.3207	1.2277	-0.0078	0.3589	0.1497	-0.2407	-0.04	0.0258	-0.2886	-0.207	0.0196	0.3449	0.0802	-0.0174	0.2847	0.0388	0.3201	-75.9378	-36.937	29.373
25	1.2332	0.2227	-0.2587	1.7212	0.0119	1.5477	0.0387	0.6544	-0.0482	-0.7995	-0.1401	-0.6118	0.0912	0.2497	0.0283	0.5849	0.1262	0.1432	0.8744	-0.0108	0.3556	-16.7431	-60.3986	12.6599
26	1.3188	0.1471	-0.4558	1.63	-0.6832	0.8638	-0.0837	0.4907	-0.2668	-0.3703	0.078	-0.1959	0.2229	0.2813	0.0344	0.396	0.0934	0.0693	0.6087	-0.1083	0.3509	-20.508	-72.0312	23.302
27	1.2612	-0.3254	0.3513	1.7929	0.2907	0.7742	0.0408	0.2596	-0.0317	-0.1056	-0.1243	0.0311	-0.0868	0.1894	0.0709	0.2762	0.0132	0.0308	0.4281	0.0501	0.2818	-32.3532	-51.2718	31.8323
28	1.4557	-0.2173	-0.1085	2.7367	0.2511	2.2396	-0.0269	0.4799	0.3904	-0.2424	-0.1304	-0.1537	-0.3453	0.2368	0.119	0.3242	-0.0175	0.0321	0.4953	0.1662	0.4048	-24.4008	-38.0231	26.7125

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 2 through 92 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 93 through 251 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 252 through 423 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 424 through 480 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 2 through 117 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 118 through 224 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 225 through 276 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 277 through 313 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 314 through 423 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 424 through 480 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 117 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 118 through 251 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 252 through 423 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 424 through 480 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 2 through 117 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 118 through 182 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 183 through 276 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 277 through 313 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 314 through 423 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 424 through 480 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 2 through 117 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 118 through 208 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 209 through 313 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 314 through 480 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 2 through 117 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 118 through 235 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 236 through 361 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 362 through 480 )

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