PDB-7x0i: Crystal structure of sugar binding protein CbpB from Clostridium ...

ID or keywords:

Entry

Database: PDB / ID: 7x0i

Title

Crystal structure of sugar binding protein CbpB from Clostridium thermocellum

Components

CbpB

Keywords

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

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

-
Download

PDBx/mmCIF format	7x0i.cif.gz	473.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7x0i.ent.gz	393.7 KB	Display	PDB format
PDBx/mmJSON format	7x0i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0i ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0i	HTTPS FTP

-
Related structure data

Related structure data	7x0gC 7x0hC 7x0jC 7x0kC 7x0lC 7x0mC 7x0nC 7x0oC 7x0pC 7x0qC 7x0rC C: citing same article (ref.)

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CbpB

B: CbpB

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

1

A: CbpB

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

2

B: CbpB

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

Unit cell

Length a, b, c (Å)	63.460, 67.350, 180.550
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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.31 %
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

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2018

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→41.118 Å / Num. obs: 163957 / % possible obs: 99.6 % / Redundancy: 6.85 % / B_iso Wilson estimate: 18.38 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.123 / R_rim(I) all: 0.133 / Χ²: 1.107 / Net I/σ(I): 12.41 / Num. measured all: 1123151 / Scaling rejects: 718

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	6.706	0.992	2.09	81592	12215	12167	0.508	1.077	99.6
1.74-1.79	6.893	0.819	3.29	81642	11874	11844	0.739	0.887	99.7
1.79-1.84	7.022	0.658	4.99	81165	11569	11558	0.87	0.711	99.9
1.84-1.9	6.89	0.71	5.74	76112	11139	11046	0.876	0.77	99.2
1.9-1.96	6.621	0.626	7.04	71967	10925	10869	0.895	0.68	99.5
1.96-2.03	6.859	0.349	8.99	71722	10485	10456	0.956	0.378	99.7
2.03-2.11	6.523	0.264	10.33	66347	10179	10172	0.972	0.288	99.9
2.11-2.19	6.595	0.212	11.85	63587	9711	9641	0.978	0.23	99.3
2.19-2.29	7.162	0.189	13.67	66740	9337	9319	0.984	0.204	99.8
2.29-2.4	7.214	0.153	15.03	64518	8966	8944	0.989	0.165	99.8
2.4-2.53	7.118	0.131	15.95	60442	8503	8491	0.991	0.142	99.9
2.53-2.69	7.005	0.111	17.33	56198	8023	8023	0.992	0.12	100
2.69-2.87	6.794	0.093	18.71	51359	7574	7559	0.994	0.101	99.8
2.87-3.1	6.159	0.08	19.29	42628	6998	6921	0.994	0.088	98.9
3.1-3.4	7.221	0.074	22.62	46797	6483	6481	0.995	0.08	100
3.4-3.8	7.185	0.071	24.15	41929	5841	5836	0.996	0.077	99.9
3.8-4.39	7.023	0.067	24.88	36209	5167	5156	0.996	0.072	99.8
4.39-5.38	6.694	0.065	24.71	29140	4355	4353	0.995	0.07	100
5.38-7.6	6.511	0.068	24.34	21474	3367	3298	0.995	0.073	98
7.6-41.118	6.354	0.071	24.6	11583	1841	1823	0.991	0.078	99

-
Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 1.7→41.118 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2022	3818	2.33 %
R_work	0.1651	160126	-
obs	0.166	163944	99.64 %

Solvent computation

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

Displacement parameters

B_iso max: 119.69 Å² / B_iso mean: 31.8072 Å² / B_iso min: 7.65 Å²

Refinement step

Cycle: final / Resolution: 1.7→41.118 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6319	0	0	732	7051
B_iso mean	-	-	-	36.52	-
Num. residues	-	-	-	-	816

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	0.3554	142	0.3516	6020	100
1.7215-1.7442	0.284	140	0.316	5862	99
1.7442-1.7681	0.3246	157	0.3341	5987	100
1.7681-1.7933	0.3199	143	0.3003	5890	100
1.7933-1.8201	0.217	135	0.2189	6014	100
1.8201-1.8485	0.2268	147	0.2052	5842	100
1.8485-1.8788	0.2588	159	0.2035	5947	100
1.8788-1.9112	0.2902	114	0.2394	5873	99
1.9112-1.946	0.2771	131	0.2223	5915	99
1.946-1.9834	0.267	157	0.1915	5976	100
1.9834-2.0239	0.214	147	0.1756	5890	100
2.0239-2.0679	0.1848	127	0.1735	5985	100
2.0679-2.116	0.2568	145	0.1697	5920	100
2.116-2.1689	0.2086	149	0.1651	5890	99
2.1689-2.2275	0.199	126	0.1612	5921	100
2.2275-2.2931	0.2375	139	0.1647	5952	100
2.2931-2.3671	0.2084	149	0.1531	5934	100
2.3671-2.4517	0.1799	139	0.1494	5931	100
2.4517-2.5498	0.1845	147	0.1493	5934	100
2.5498-2.6659	0.2141	138	0.1493	5964	100
2.6659-2.8064	0.1637	152	0.1496	5980	100
2.8064-2.9822	0.2128	141	0.1447	5908	99
2.9822-3.2123	0.1971	144	0.1422	5887	99
3.2123-3.5354	0.181	142	0.1369	5946	100
3.5354-4.0467	0.1584	148	0.1281	5930	100
4.0467-5.0968	0.1488	129	0.1257	5948	100
5.0968-41.118	0.1891	131	0.1724	5880	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	1.8483	0.4376	0.6129	5.8284	0.8969	1.8703	-0.0402	-0.359	-0.2696	0.4281	0.0919	-0.1423	0.2002	-0.0008	-0.0412	0.2265	0.0755	0.0099	0.2415	0.0462	0.1435	24.6352	-28.2502	-21.1592
2	3.4541	0.0513	0.648	3.2293	0.0146	3.1823	-0.0196	-0.0753	-0.0222	0.0817	0.1212	-0.3507	-0.106	0.3409	-0.0578	0.0991	0.0298	-0.0216	0.149	-0.0253	0.1736	32.596	-20.3142	-31.9712
3	6.6383	-1.7247	1.9933	1.0605	-0.4426	1.1381	0.02	0.1577	0.1799	-0.0499	-0.0261	-0.0823	0.0174	0.1331	0.0087	0.1317	0.0085	-0.0078	0.0891	-0.031	0.114	16.2711	-16.7045	-39.7111
4	3.1741	0.6139	2.1295	0.7958	0.208	4.0675	-0.0155	0.0733	0.0588	-0.0416	0.0226	0.1289	-0.0298	-0.0426	0.0055	0.1315	0.0211	0.0001	0.0419	-0.0215	0.1323	-0.2207	-6.5226	-42.9747
5	5.9467	2.1323	0.9816	3.9688	-0.44	2.7637	0.0076	0.244	-0.0917	0.0303	-0.0252	-0.3404	0.0507	0.4304	0.0135	0.0982	0.0238	-0.0148	0.1351	-0.0068	0.1111	22.2127	-2.1547	-40.6251
6	2.411	1.0582	-0.1114	2.9532	-0.854	1.5234	0.0751	-0.1146	-0.0527	0.0506	-0.0538	0.1598	0.0773	-0.0253	-0.0338	0.1077	0.0146	-0.0208	0.0826	-0.0371	0.0847	3.5846	-9.238	-35.3617
7	2.0707	-0.3688	0.6491	1.1843	-0.4623	1.1785	0.1189	0.1735	-0.1213	-0.0213	-0.0507	-0.0005	0.1187	0.1716	-0.0608	0.1592	0.0232	-0.0201	0.0907	-0.0551	0.0987	16.02	-17.8474	-37.7188
8	6.8393	-0.7953	3.6748	2.3305	-1.0709	5.608	-0.0366	0.0615	-0.4352	0.1165	0.1141	0.0356	0.1401	0.155	-0.0952	0.1366	0.0356	0.001	0.0757	-0.0076	0.1782	23.1697	-31.0108	-34.4898
9	1.1133	0.1171	0.0272	2.9114	0.5719	0.4839	0.0417	-0.0188	-0.0072	0.0295	-0.0334	0.0153	0.0096	0.0335	-0.0083	0.1247	0.012	-0.0113	0.1132	0.0102	0.0671	15.5025	-8.5232	-37.1427
10	5.0351	-5.5916	3.6369	7.2192	-2.8605	3.9967	0.0025	0.1599	0.7114	0.1039	-0.0727	-0.8039	-0.175	0.3708	0.1278	0.1538	-0.0558	-0.0253	0.148	-0.0296	0.2746	25.6592	6.9984	-33.5069
11	2.3151	-0.8666	-0.1281	2.488	-0.4746	1.1136	-0.0158	-0.1722	-0.119	0.153	0.0176	0.2365	-0.0821	-0.1044	-0.0502	0.174	0.0095	0.038	0.1653	-0.0275	0.1079	-11.6503	9.9878	-17.2549
12	1.3152	0.1188	0.2958	2.7293	-1.17	4.4537	-0.0733	-0.5468	-0.8001	0.3796	0.1605	0.2325	0.52	0.2292	0.0415	0.354	0.1189	0.0626	0.3951	0.1915	0.342	5.8663	-14.4136	-3.3763
13	3.0863	-0.396	0.284	2.4474	1.0095	2.0686	-0.2118	-0.5042	-0.3612	0.2169	0.2358	0.0739	0.1366	0.205	-0.0177	0.2136	0.0384	0.028	0.2468	0.0486	0.1218	3.868	-5.9201	-8.7646
14	2.7168	-1.7325	0.0701	1.9935	0.0808	0.5034	-0.1474	-0.4057	-0.0457	0.2863	0.2026	0.0639	-0.0048	0.0484	-0.0741	0.2392	0.0049	0.0367	0.2185	-0.0219	0.0898	-2.0235	5.5287	-10.0801

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 103 )	A	49 - 103
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 104 through 147 )	A	104 - 147
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 177 )	A	148 - 177
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 178 through 220 )	A	178 - 220
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 221 through 248 )	A	221 - 248
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 249 through 308 )	A	249 - 308
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 309 through 345 )	A	309 - 345
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 346 through 380 )	A	346 - 380
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 381 through 435 )	A	381 - 435
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 436 through 458 )	A	436 - 458
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 49 through 177 )	B	49 - 177
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 178 through 220 )	B	178 - 220
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 221 through 319 )	B	221 - 319
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 320 through 454 )	B	320 - 454

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi