PDB-7x0n: Crystal structure of sugar binding protein CbpB complexed wtih la...

ID or keywords:

Entry

Database: PDB / ID: 7x0n

Title

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

Components

CbpB

Keywords

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

Function / homology

beta-laminaribiose

Function and homology information

Biological species

Acetivibrio thermocellus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.68 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	7x0n.cif.gz	475.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7x0n_validation.pdf.gz	980.6 KB	Display	wwPDB validaton report
Full document	7x0n_full_validation.pdf.gz	983 KB	Display
Data in XML	7x0n_validation.xml.gz	36.9 KB	Display
Data in CIF	7x0n_validation.cif.gz	57 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0n ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0n	HTTPS FTP

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Related structure data

Related structure data	7x0gC 7x0hC 7x0iC 7x0jC 7x0kC 7x0lC 7x0mC 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)	72.750, 46.440, 116.490
Angle α, β, γ (deg.)	90.000, 106.580, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#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-(1-3)-beta-D-glucopyranose

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

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.09 Å³/Da / Density % sol: 41.14 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2% Tacsimate pH 4.0, 0.1 M sodium acetate trihydrate pH 4.6, 16% 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: BL17U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 4, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.68→25.707 Å / Num. obs: 148751 / % possible obs: 89.2 % / Redundancy: 1.874 % / B_iso Wilson estimate: 20.27 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.064 / Χ²: 0.988 / Net I/σ(I): 11.25 / Num. measured all: 278714 / Scaling rejects: 12

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
1.68-1.72	1.875	0.426	2.43	21272	12431	11347	0.665	0.593	91.3
1.72-1.77	1.886	0.364	2.89	20886	12011	11077	0.712	0.507	92.2
1.77-1.82	1.867	0.286	3.6	19894	11641	10653	0.805	0.4	91.5
1.82-1.88	1.868	0.231	4.41	19077	11345	10214	0.867	0.322	90
1.88-1.94	1.863	0.182	5.56	17834	11059	9571	0.91	0.254	86.5
1.94-2.01	1.872	0.142	6.91	18519	10695	9894	0.948	0.197	92.5
2.01-2.08	1.858	0.106	8.6	17398	10209	9366	0.969	0.148	91.7
2.08-2.17	1.86	0.088	10.04	16431	9798	8833	0.977	0.123	90.2
2.17-2.27	1.832	0.078	11.4	15215	9542	8304	0.982	0.109	87
2.27-2.38	1.875	0.065	12.67	15124	9009	8065	0.987	0.091	89.5
2.38-2.5	1.892	0.056	14.33	14699	8668	7769	0.99	0.077	89.6
2.5-2.66	1.886	0.048	15.77	13721	8132	7275	0.992	0.066	89.5
2.66-2.84	1.87	0.04	18.07	12047	7629	6441	0.994	0.056	84.4
2.84-3.07	1.896	0.035	20.01	12126	7154	6397	0.995	0.049	89.4
3.07-3.36	1.886	0.032	21.98	10979	6554	5821	0.996	0.044	88.8
3.36-3.76	1.871	0.03	23.74	9436	5935	5043	0.996	0.041	85
3.76-4.34	1.906	0.027	25.21	8337	5224	4374	0.996	0.037	83.7
4.34-5.31	1.905	0.026	25.69	7363	4412	3865	0.996	0.036	87.6
5.31-7.51	1.909	0.026	25.63	5449	3409	2854	0.997	0.036	83.7
7.51-25.707	1.831	0.023	26.08	2907	1868	1588	0.997	0.032	85

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
xia2		data scaling
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.68→25.707 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2099	3652	2.46 %
R_work	0.1734	145051	-
obs	0.1743	148703	89.24 %

Solvent computation

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

Displacement parameters

B_iso max: 106.95 Å² / B_iso mean: 29.4763 Å² / B_iso min: 9.58 Å²

Refinement step

Cycle: final / Resolution: 1.68→25.707 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6310	0	90	804	7204
B_iso mean	-	-	16.91	33.4	-
Num. residues	-	-	-	-	818

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 (%)
1.68-1.7021	0.2942	138	0.254	5638	90
1.7021-1.7254	0.2428	151	0.247	5827	92
1.7254-1.7501	0.2576	155	0.2449	5665	93
1.7501-1.7762	0.2976	138	0.2326	5793	92
1.7762-1.8039	0.2791	132	0.2248	5749	92
1.8039-1.8335	0.2326	144	0.2209	5730	91
1.8335-1.8651	0.2755	161	0.2132	5644	90
1.8651-1.899	0.2308	124	0.2114	5428	87
1.899-1.9355	0.287	138	0.2136	5458	86
1.9355-1.975	0.284	147	0.2097	5705	92
1.975-2.0179	0.2336	139	0.195	5855	93
2.0179-2.0649	0.2296	143	0.1858	5668	92
2.0649-2.1165	0.2366	128	0.1902	5764	91
2.1165-2.1737	0.2035	151	0.1768	5494	90
2.1737-2.2376	0.2385	132	0.1814	5544	88
2.2376-2.3098	0.2081	145	0.1784	5340	86
2.3098-2.3923	0.2246	148	0.1827	5718	92
2.3923-2.488	0.1885	145	0.1764	5599	90
2.488-2.6011	0.2151	149	0.1784	5615	89
2.6011-2.7381	0.2102	135	0.1704	5505	88
2.7381-2.9094	0.2001	136	0.1731	5213	83
2.9094-3.1337	0.2328	151	0.1737	5629	91
3.1337-3.4484	0.2161	132	0.1685	5536	88
3.4484-3.9459	0.2043	131	0.1498	5135	82
3.9459-4.9655	0.1357	135	0.1264	5485	88
4.9655-25.7	0.1552	124	0.1446	5314	85

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	0.2146	0.05	0.5525	3.0104	1.6349	2.3319	0.1861	-0.8111	0.7409	0.1431	0.0478	-0.5793	-0.2171	0.39	-0.2311	0.1892	-0.0935	-0.0105	0.5378	-0.2289	0.4876	18.25	-2.1736	42.5707
2	2.5561	0.3072	-0.1153	1.3323	-0.6609	1.4315	0.1682	-0.7481	0.1996	0.213	-0.0922	0.0539	0.0307	0.1551	-0.0156	0.1421	-0.0284	-0.0019	0.2688	-0.0567	0.1444	6.3461	-9.0083	36.9603
3	2.3331	0.3065	-0.9235	2.245	-0.3587	2.5188	0.0478	0.4872	0.1827	-0.2176	-0.118	-0.0691	-0.0172	0.2263	0.0682	0.1488	0.0099	0.0279	0.2271	0.0418	0.1373	10.4098	-6.409	5.5039
4	2.9558	0.2039	-0.1329	0.671	-0.1595	0.5987	0.1146	-0.1579	0.2117	0.0379	-0.0957	-0.0176	-0.0224	0.0734	-0.0262	0.1227	-0.0086	0.005	0.0817	-0.014	0.1369	8.1863	-8.5768	23.2219
5	2.3524	-0.1799	-0.4902	0.252	0.0026	1.0791	0.1091	-0.0462	0.2499	0.0396	-0.0427	0.0245	-0.0503	0.0116	-0.0474	0.1643	0.0007	0.0073	0.1021	-0.0026	0.1978	5.0168	-9.4127	23.0765
6	1.5391	-0.2475	-1.3522	0.9528	-0.2301	2.6152	-0.0231	0.0677	-0.5948	0.1332	-0.0035	0.3654	0.2817	-0.212	0.3371	0.2646	0.0231	-0.017	0.1696	-0.0565	0.4709	-1.5312	-29.677	21.7108
7	0.5829	0.0389	-0.3987	2.0261	-0.2373	4.4086	0.0735	-0.2616	0.0234	0.0408	-0.2738	0.3816	0.3764	-0.3836	0.1639	0.2537	0.0833	-0.0555	0.5519	-0.1746	0.2743	32.6923	-7.8784	45.0357
8	0.7014	0.1163	-0.5555	1.4319	0.5412	1.9954	-0.129	-0.3879	0.4702	0.2076	-0.002	-0.2358	-0.2232	-0.1004	-0.0247	0.281	0.0915	-0.1152	0.3372	-0.1815	0.2565	44.071	-0.3245	40.0905
9	1.5586	0.0892	0.7932	1.8261	1.1992	1.7963	-0.1767	-0.2592	0.1661	0.0505	0.1532	-0.2018	-0.1681	-0.0093	0.0161	0.1735	0.0346	-0.0102	0.1733	-0.0335	0.1205	45.7408	-15.2893	29.7376
10	2.4875	-0.4598	0.6617	1.3681	-0.289	1.4761	-0.1191	0.0415	-0.1015	-0.0126	0.1203	0.0047	0.0451	-0.1043	0.0051	0.1444	-0.007	0.0193	0.1349	-0.0144	0.1158	40.1836	-25.6533	12.7633
11	2.053	-0.0494	0.0583	1.092	0.1798	0.7713	-0.1008	-0.14	0.1431	0.0966	0.0476	0.0461	-0.057	-0.1187	0.0594	0.1387	0.0355	-0.0162	0.1074	-0.023	0.0902	42.5061	-13.9681	18.0361
12	1.0606	-0.305	0.0383	0.7065	0.4407	1.1474	-0.158	-0.3373	0.1054	0.1817	0.0812	0.0032	0.0234	-0.0542	0.0198	0.1714	0.0559	-0.0032	0.1765	-0.0398	0.1186	43.6263	-15.0634	30.2397
13	0.6883	0.34	-0.1398	1.797	1.2196	2.2144	-0.0951	-0.7186	-0.0156	0.3746	-0.0675	-0.1595	0.3236	-0.1821	-0.0033	0.2972	0.1062	-0.0579	0.4434	-0.0723	0.1142	43.377	-13.4889	45.8105
14	1.1085	-0.2226	0.4681	0.5373	0.347	1.7801	-0.1303	-0.1456	0.0686	0.1558	0.1284	-0.0569	-0.1014	-0.1519	0.069	0.128	0.0322	0.0023	0.1264	-0.0285	0.1347	46.0932	-11.6335	22.1752
15	2.922	1.9044	3.0237	3.69	4.0618	7.8005	-0.2245	0.0895	0.5628	-0.1278	0.0798	-0.0795	-0.5672	0.3056	0.0593	0.2014	-0.0136	-0.0274	0.1331	0.0437	0.2784	52.6604	2.6527	11.9023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 49 through 77 )	A	49 - 77
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 78 through 177 )	A	78 - 177
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 178 through 218 )	A	178 - 218
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 219 through 369 )	A	219 - 369
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 370 through 435 )	A	370 - 435
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 436 through 457 )	A	436 - 457
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 49 through 77 )	B	49 - 77
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 78 through 147 )	B	78 - 147
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 148 through 177 )	B	148 - 177
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 178 through 218 )	B	178 - 218
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 219 through 308 )	B	219 - 308
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 309 through 345 )	B	309 - 345
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 346 through 380 )	B	346 - 380
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 381 through 435 )	B	381 - 435
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 436 through 457 )	B	436 - 457

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