PDB-7x0j: Crystal structure of sugar binding protein CbpB complexed wtih ce...

ID or keywords:

Entry

Database: PDB / ID: 7x0j

Title

Crystal structure of sugar binding protein CbpB complexed wtih cellobiose from Clostridium thermocellum

Components

CbpB

Keywords

SUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin

Function / homology

beta-cellobiose

Function and homology information

Biological species

Acetivibrio thermocellus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Dong, S. / Yao, X. / Feng, Y.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	32070125	China
National Natural Science Foundation of China (NSFC)	32170051	China
National Natural Science Foundation of China (NSFC)	32171203	China

Citation

Journal: Mbio / Year: 2022
Title: Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum.
Authors: Yan, F. / Dong, S. / Liu, Y.J. / Yao, X. / Chen, C. / Xiao, Y. / Bayer, E.A. / Shoham, Y. / You, C. / Cui, Q. / Feng, Y.

History

Deposition	Feb 22, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 14, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7x0j.cif.gz	473.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7x0j.ent.gz	394.5 KB	Display	PDB format
PDBx/mmJSON format	7x0j.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/x0/7x0j ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0j	HTTPS FTP

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Related structure data

Related structure data	7x0gC 7x0hC 7x0iC 7x0kC 7x0lC 7x0mC 7x0nC 7x0oC 7x0pC 7x0qC 7x0rC 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: CbpB

B: CbpB

hetero molecules

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

1

A: CbpB

hetero molecules

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

2

B: CbpB

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.950, 72.820, 230.600
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

CbpB

Mass: 45245.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acetivibrio thermocellus (bacteria) / Production host:

Escherichia coli BL21(DE3) (bacteria)

#2: Polysaccharide

beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 816 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

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: 2.13 Å³/Da / Density % sol: 42.3 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M Sodium acetate, pH 4.5, 18% w/v Polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.7→45.2 Å / Num. obs: 162939 / % possible obs: 99.1 % / Redundancy: 3.371 % / B_iso Wilson estimate: 22.16 Å² / CC_1/2: 0.985 / R_merge(I) obs: 0.132 / R_rim(I) all: 0.157 / Χ²: 1.037 / Net I/σ(I): 5.82 / Num. measured all: 549323

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	3.444	0.714	1.65	41634	12104	12088	0.584	0.848	99.9
1.74-1.79	3.378	0.578	2.03	39937	11851	11824	0.697	0.689	99.8
1.79-1.84	3.239	0.466	2.44	37357	11588	11533	0.764	0.56	99.5
1.84-1.9	3.236	0.452	2.9	36117	11194	11160	0.802	0.545	99.7
1.9-1.96	3.486	0.411	3.62	37751	10855	10829	0.77	0.488	99.8
1.96-2.03	3.524	0.27	4.61	36868	10485	10462	0.906	0.32	99.8
2.03-2.11	3.486	0.226	5.36	35155	10131	10086	0.927	0.269	99.6
2.11-2.19	3.44	0.193	5.99	33465	9796	9729	0.942	0.229	99.3
2.19-2.29	3.321	0.23	6.18	30674	9332	9237	0.904	0.276	99
2.29-2.4	3.169	0.162	6.74	27741	8919	8754	0.944	0.195	98.2
2.4-2.53	3.371	0.149	7.58	28439	8551	8436	0.954	0.178	98.7
2.53-2.69	3.452	0.138	8.31	27506	8046	7967	0.96	0.164	99
2.69-2.87	3.378	0.126	8.84	25147	7551	7444	0.96	0.151	98.6
2.87-3.1	3.319	0.118	9.21	22699	6972	6839	0.966	0.141	98.1
3.1-3.4	3.116	0.11	9.28	19608	6469	6293	0.969	0.133	97.3
3.4-3.8	3.288	0.104	9.83	18805	5877	5720	0.974	0.124	97.3
3.8-4.39	3.5	0.099	10.58	17665	5121	5047	0.976	0.117	98.6
4.39-5.38	3.462	0.092	10.7	14960	4373	4321	0.977	0.109	98.8
5.38-7.6	3.253	0.078	10.3	10885	3357	3346	0.985	0.093	99.7
7.6-45.2	3.788	0.074	11.41	6910	1840	1824	0.987	0.087	99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→45.2 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2112	3751	2.3 %
R_work	0.1798	159161	-
obs	0.1805	162912	99.09 %

Solvent computation

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

Displacement parameters

B_iso max: 132.67 Å² / B_iso mean: 31.2298 Å² / B_iso min: 10.65 Å²

Refinement step

Cycle: final / Resolution: 1.7→45.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6263	0	46	816	7125
B_iso mean	-	-	16.56	37.56	-
Num. residues	-	-	-	-	811

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.7-1.7215	0.4297	139	0.4066	5884	100
1.7215-1.7442	0.4367	137	0.3894	5926	100
1.7442-1.7681	0.3921	140	0.3542	5983	100
1.7681-1.7933	0.3636	140	0.3204	5880	100
1.7933-1.8201	0.24	139	0.2809	5950	100
1.8201-1.8485	0.2703	136	0.2448	5883	99
1.8485-1.8788	0.2688	143	0.2279	5959	100
1.8788-1.9112	0.2327	141	0.222	6015	100
1.9112-1.946	0.2595	139	0.2295	5848	100
1.946-1.9834	0.2636	143	0.2133	5963	100
1.9834-2.0239	0.2573	139	0.2157	5937	100
2.0239-2.0679	0.2264	140	0.207	5920	100
2.0679-2.116	0.2198	139	0.209	5875	99
2.116-2.1689	0.2388	138	0.1888	5950	99
2.1689-2.2276	0.196	138	0.1886	5897	100
2.2276-2.2931	0.228	139	0.1976	5920	99
2.2931-2.3671	0.1984	136	0.183	5788	98
2.3671-2.4517	0.1946	139	0.1763	5859	98
2.4517-2.5499	0.2212	140	0.1807	5933	99
2.5499-2.6659	0.2009	143	0.1744	5849	99
2.6659-2.8064	0.1836	138	0.1713	5855	98
2.8064-2.9822	0.213	135	0.1724	5843	99
2.9822-3.2124	0.2041	140	0.1632	5830	98
3.2124-3.5356	0.2171	138	0.1542	5816	97
3.5356-4.0469	0.1738	140	0.1374	5812	98
4.0469-5.0976	0.1665	138	0.1228	5890	99
5.0976-45.2	0.1586	134	0.1494	5896	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	1.3744	-0.3757	1.3271	2.9906	0.2794	2.528	0.0241	0.1988	0.1039	-0.1491	-0.0236	-0.1729	-0.1302	0.5255	0.1359	0.1312	-0.0385	0.013	0.231	0.0373	0.1653	-6.7202	-36.9242	-43.5212
2	1.5066	0.114	-0.1145	1.3825	-0.3362	2.062	-0.2137	-0.7237	-0.534	0.1799	0.1004	-0.0151	0.3446	0.0275	0.0479	0.3007	0.0394	0.0557	0.3797	0.181	0.2976	-27.2088	-3.8433	-9.9782
3	4.6719	0.4462	-0.5853	2.7851	-0.786	4.3857	-0.0349	-0.5732	0.0676	0.3266	0.0476	0.1703	-0.2863	-0.0618	0.0132	0.2089	0.0127	0.0293	0.1971	0.0227	0.1007	-30.6775	10.8152	-13.6466
4	2.9553	-1.4245	-2.0082	2.4426	1.4433	2.3562	-0.0289	-0.221	-0.0285	0.0314	0.0738	-0.1432	-0.0822	0.2254	-0.0886	0.1452	-0.0474	-0.0242	0.1463	0.0196	0.1281	-17.7005	7.0874	-25.4751
5	3.7665	0.1408	-0.0239	3.9051	0.4773	3.1653	-0.0223	0.1111	-0.4064	-0.2402	0.0152	-0.3301	0.4111	0.2167	-0.006	0.187	0.0027	0.0276	0.1592	-0.0445	0.234	-9.2717	0.7625	-43.2743
6	1.7181	-1.0511	-0.4392	2.7249	-0.445	1.7623	-0.024	-0.0185	0.0128	-0.0428	0.1071	0.215	0.0192	-0.1197	-0.0895	0.1362	-0.0484	-0.0125	0.1669	0.0021	0.1342	-27.2645	13.3963	-35.6633
7	3.8211	-0.1357	0.3677	2.8758	-0.3328	4.8581	0.0266	0.3186	-0.3172	-0.3327	0.0174	-0.2999	0.4628	0.1725	-0.0245	0.1537	-0.0511	-0.013	0.1944	-0.057	0.1445	-21.364	3.5444	-45.7862
8	2.1969	-1.1895	0.0305	5.3861	-1.3177	1.4554	-0.1472	-0.1071	-0.3495	0.0395	0.0363	-0.247	0.1095	0.0284	0.1154	0.1321	-0.0342	0.0101	0.1409	-0.0041	0.2053	-11.4329	-2.253	-30.9053
9	1.7369	-0.4163	0.2099	1.272	-0.2856	1.0284	-0.0812	-0.4806	-0.0749	0.2175	0.0849	-0.0907	-0.0924	0.092	0.05	0.1815	-0.0087	-0.0121	0.2354	0.0363	0.1197	-18.2378	7.6386	-14.7731
10	1.8179	-1.1622	-1.9148	0.944	1.929	7.3985	-0.0037	0.2237	-0.2033	-0.0687	0.0084	0.161	0.2049	-0.0221	0.0403	0.1767	-0.0833	-0.0375	0.2161	-0.046	0.2037	-33.5825	5.8321	-42.8608
11	2.1612	0.1675	-0.3694	1.2008	0.2007	1.7644	0.0815	-0.2518	0.2038	0.1943	-0.0376	0.0728	-0.1845	-0.0137	-0.0534	0.2222	-0.0385	0.008	0.1809	-0.0251	0.1482	-24.4229	-26.8864	-14.7857
12	2.258	-0.4942	2.1823	0.7809	-0.9912	5.4316	0.0658	0.0718	0.0296	-0.0583	-0.0623	0.0228	0.0451	-0.283	-0.0937	0.1399	-0.0322	0.013	0.1287	0.0007	0.1357	-29.8867	-34.3596	-30.443
13	7.5877	-2.693	1.8485	8.6843	-3.1682	4.8939	0.3399	0.3106	-0.1838	-0.1467	-0.1686	0.2822	-0.0303	-0.4431	-0.153	0.1707	-0.005	-0.0389	0.2765	0.0171	0.1108	-34.3915	-37.7493	-51.7427
14	3.935	-3.3026	5.2121	4.7505	-3.4807	8.4157	-0.0404	0.3794	0.6161	-0.3405	-0.0571	0.309	-0.4825	-0.0199	0.2283	0.3103	0.0027	0.0041	0.3085	0.122	0.3083	-28.2672	-23.5345	-49.8276
15	1.7471	-0.1433	0.3126	0.9718	1.2663	3.416	0.078	-0.0062	0.0226	0.0005	-0.0269	-0.1907	0.0376	0.0163	-0.0489	0.1364	-0.0421	-0.0159	0.1355	0.024	0.1315	-17.1052	-41.8411	-35.4956
16	2.3501	-1.6992	-0.7461	1.8923	1.0833	1.2079	0.1172	0.2001	0.2493	-0.0998	-0.0513	-0.0192	-0.3565	-0.0391	-0.1069	0.2213	-0.0213	0.007	0.1812	0.0628	0.1541	-22.3797	-29.7036	-46.7882
17	2.8811	-2.0939	-0.6481	3.6114	0.7735	1.8069	0.115	0.082	0.2713	-0.0481	-0.0769	0.0522	-0.2978	-0.2396	-0.0226	0.1795	0.0039	0.0109	0.2124	0.0374	0.1489	-34.9069	-28.1421	-38.2407
18	5.0507	-0.0779	2.2535	1.614	0.2143	6.3544	0.045	-0.5266	0.2254	0.2756	-0.0953	0.0434	-0.2217	-0.3283	0.0871	0.1941	-0.038	0.0181	0.1381	-0.0356	0.1363	-30.1299	-28.7	-12.0669
19	0.2854	0.2004	0.2818	0.3923	0.0893	1.0952	0.049	-0.0701	0.0609	0.0172	-0.047	0.0329	-0.0341	-0.1341	-0.003	0.1721	-0.0194	-0.0112	0.2064	0.0132	0.195	-27.7581	-35.4202	-30.9431

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 428 through 454 )	B	428 - 454
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 103 )	A	49 - 103
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 147 )	A	104 - 147
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 148 through 177 )	A	148 - 177
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 218 )	A	178 - 218
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 219 through 248 )	A	219 - 248
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 249 through 275 )	A	249 - 275
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 276 through 332 )	A	276 - 332
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 333 through 408 )	A	333 - 408
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 409 through 454 )	A	409 - 454
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 50 through 147 )	B	50 - 147
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 148 through 177 )	B	148 - 177
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 178 through 198 )	B	178 - 198
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 199 through 218 )	B	199 - 218
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 219 through 248 )	B	219 - 248
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 249 through 289 )	B	249 - 289
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 290 through 332 )	B	290 - 332
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 333 through 369 )	B	333 - 369
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 370 through 427 )	B	370 - 427

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