PDB-7x0h: Crystal structure of sugar binding protein CbpA complexed wtih gl...

ID or keywords:

Entry

Database: PDB / ID: 7x0h

Title

Crystal structure of sugar binding protein CbpA complexed wtih glucose from Clostridium thermocellum

Components

CbpA

Keywords

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

Function / homology

beta-D-glucopyranose

Function and homology information

Biological species

Acetivibrio thermocellus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

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

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	32171203	China
National Natural Science Foundation of China (NSFC)	32070125	China
National Natural Science Foundation of China (NSFC)	32170051	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	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7x0h.cif.gz	635.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7x0h.ent.gz	534 KB	Display	PDB format
PDBx/mmJSON format	7x0h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7x0h_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7x0h_full_validation.pdf.gz	1.8 MB	Display
Data in XML	7x0h_validation.xml.gz	55.4 KB	Display
Data in CIF	7x0h_validation.cif.gz	85.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0h ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0h	HTTPS FTP

-
Related structure data

Related structure data	7x0gC 7x0iC 7x0jC 7x0kC 7x0lC 7x0mC 7x0nC 7x0oC 7x0pC 7x0qC 7x0rC 2h3hS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: CbpA

B: CbpA

C: CbpA

D: CbpA

hetero molecules

124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CbpA

hetero molecules

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

2

B: CbpA

hetero molecules

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

3

C: CbpA

hetero molecules

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

4

D: CbpA

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.873, 234.616, 196.325
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein

CbpA

Mass: 30877.381 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: GB CP002416.1 / Source: (gene. exp.)

Acetivibrio thermocellus (bacteria) / Production host:

Escherichia coli BL21(DE3) (bacteria)

#2: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1531 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.54 Å³/Da / Density % sol: 65.22 % Description: The entry contains friedel pairs in I_plus/minus columns
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 2.0 M Ammonium sulfate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.9785 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9785 Å / Relative weight: 1

Reflection

Resolution: 1.85→48.485 Å / Num. obs: 148842 / % possible obs: 100 % / Redundancy: 6.93 % / B_iso Wilson estimate: 16.97 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.164 / R_rim(I) all: 0.177 / Χ²: 0.842 / Net I/σ(I): 9.56 / Num. measured all: 2002568 / Scaling rejects: 125

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
1.85-1.9	7.075	1.005	2	151959	21481	21477	0.823	1.085	100
1.9-1.95	7.077	0.825	2.46	147021	20778	20774	0.876	0.891	100
1.95-2.01	6.987	0.686	2.94	141479	20254	20250	0.914	0.741	100
2.01-2.07	6.886	0.574	3.43	135291	19652	19648	0.934	0.621	100
2.07-2.14	6.734	0.462	4.15	128321	19056	19055	0.957	0.5	100
2.14-2.21	6.317	0.377	4.78	116898	18506	18506	0.965	0.411	100
2.21-2.29	7.177	0.329	5.81	128081	17846	17846	0.98	0.355	100
2.29-2.39	7.125	0.281	6.71	121903	17112	17108	0.984	0.303	100
2.39-2.49	7.096	0.262	7.1	116428	16407	16407	0.986	0.283	100
2.49-2.62	7.02	0.225	8.19	110562	15750	15749	0.989	0.243	100
2.62-2.76	6.751	0.186	9.65	100733	14926	14922	0.99	0.201	100
2.76-2.93	6.607	0.151	11.45	93400	14137	14137	0.993	0.164	100
2.93-3.13	7.282	0.125	14.25	96578	13263	13263	0.996	0.134	100
3.13-3.38	7.155	0.093	17.91	88161	12322	12322	0.997	0.1	100
3.38-3.7	6.997	0.071	21.49	79526	11370	11366	0.998	0.077	100
3.7-4.14	6.288	0.057	23.08	64749	10301	10298	0.998	0.062	100
4.14-4.78	7.199	0.05	27.48	65277	9069	9067	0.999	0.054	100
4.78-5.85	7.22	0.055	25.84	55408	7674	7674	0.999	0.059	100
5.85-8.27	6.499	0.054	25.51	38333	5906	5898	0.999	0.059	99.9
8.27-48.485	7.036	0.033	35.94	22460	3224	3192	1	0.036	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:

MOLECULAR REPLACEMENT
Starting model: 2H3H

2h3h

Resolution: 1.85→48.485 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.6 / Stereochemistry target values: ML
Details: he entry contains friedel pairs in I_plus/minus columns

	R_factor	Num. reflection	% reflection
R_free	0.1882	7280	4.89 %
R_work	0.1619	141562	-
obs	0.1632	148842	99.9 %

Solvent computation

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

Displacement parameters

B_iso max: 121.29 Å² / B_iso mean: 23.6196 Å² / B_iso min: 8.13 Å²

Refinement step

Cycle: final / Resolution: 1.85→48.485 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8512	0	96	1531	10139
B_iso mean	-	-	14.65	34.33	-
Num. residues	-	-	-	-	1148

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 (%)
1.85-1.871	0.2631	225	0.2326	4671	100
1.871-1.8931	0.2538	228	0.2199	4721	100
1.8931-1.9161	0.2343	248	0.2043	4643	100
1.9161-1.9404	0.2495	239	0.1977	4696	100
1.9404-1.9659	0.2161	255	0.196	4662	100
1.9659-1.9929	0.2212	233	0.1889	4691	100
1.9929-2.0213	0.2068	246	0.189	4684	100
2.0213-2.0515	0.2256	232	0.1895	4721	100
2.0515-2.0836	0.2287	236	0.1882	4634	100
2.0836-2.1177	0.2243	212	0.1803	4731	100
2.1177-2.1542	0.1905	270	0.1743	4646	100
2.1542-2.1934	0.2145	253	0.1679	4672	100
2.1934-2.2356	0.1862	231	0.1549	4757	100
2.2356-2.2812	0.1787	248	0.1524	4649	100
2.2812-2.3308	0.1701	241	0.1534	4683	100
2.3308-2.385	0.1843	274	0.1483	4675	100
2.385-2.4447	0.184	248	0.1479	4704	100
2.4447-2.5108	0.1903	223	0.1544	4723	100
2.5108-2.5847	0.188	232	0.1619	4701	100
2.5847-2.6681	0.1954	253	0.1577	4729	100
2.6681-2.7634	0.1926	249	0.1644	4702	100
2.7634-2.8741	0.21	238	0.1593	4733	100
2.8741-3.0049	0.1953	247	0.1641	4745	100
3.0049-3.1632	0.183	264	0.1685	4722	100
3.1632-3.3614	0.1864	271	0.1586	4685	100
3.3614-3.6208	0.1606	236	0.1467	4802	100
3.6208-3.9851	0.162	240	0.1372	4778	100
3.9851-4.5613	0.1474	229	0.1243	4808	100
4.5613-5.7453	0.1501	223	0.1419	4844	100
5.7453-48.48	0.1879	256	0.1845	4950	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	1.0861	-1.0045	0.3679	3.6199	-0.1889	1.4639	-0.1062	-0.0998	-0.0967	0.3765	0.1244	0.0597	0.0023	-0.0284	-0.0134	0.162	0.0285	-0.0041	0.0977	0.0139	0.0833	10.6515	25.7375	-8.7861
2	1.0769	-0.7499	0.1749	1.9685	-0.2773	0.8037	-0.0833	-0.0359	0.1618	0.306	0.0338	-0.3338	-0.1031	0.0743	0.0455	0.1571	0.0152	-0.0576	0.0947	-0.0106	0.1718	18.3518	35.4702	-12.4338
3	1.2065	-0.3643	0.3452	2.1899	0.7201	1.2971	-0.0355	0.0491	0.0433	-0.1335	-0.0362	0.0824	-0.1612	-0.0566	0.0417	0.1482	0.0163	-0.0052	0.0798	0.0112	0.1185	-2.8185	49.3688	-23.9806
4	2.1924	-1.1297	0.3461	1.2698	0.0373	0.4602	-0.0093	-0.0196	0.0628	0.0609	-0.0098	0.0692	-0.0153	-0.0784	0.0048	0.1187	0.0057	0.0039	0.0894	0.0063	0.1105	-0.5788	31.7979	-18.9711
5	1.6313	0.49	0.3165	3.0258	-0.5828	1.2665	-0.0725	0.0644	0.0623	-0.2445	0.0413	0.0273	-0.0291	0.0187	0.0258	0.1538	-0.0306	-0.0096	0.0953	0.0022	0.073	24.5358	27.6688	7.5218
6	1.1153	0.1652	0.1101	2.4163	0.3431	2.0107	0.0342	-0.0328	0.1095	-0.06	-0.0255	0.1832	-0.0179	-0.1874	0.0223	0.089	-0.0141	-0.0151	0.0881	0.0074	0.1201	18.1982	32.4751	16.7927
7	3.5286	0.8875	1.9447	1.6162	-0.1433	2.5127	-0.0411	-0.1232	0.0256	0.1426	-0.0516	-0.074	-0.0934	-0.0075	0.0889	0.1544	-0.0098	-0.0052	0.0661	-0.003	0.1244	38.7365	43.4787	28.8993
8	1.5173	-0.1265	0.653	2.9101	-0.7134	1.4885	-0.0031	0.0914	0.0421	0.0403	0.0377	-0.1837	-0.0662	0.1232	-0.016	0.1575	-0.0292	0.0094	0.0966	-0.0005	0.1431	42.5485	50.4582	18.7042
9	2.7416	1.8967	-0.161	5.4991	0.0141	1.9812	-0.0662	0.2283	0.0205	-0.276	0.0701	-0.462	-0.0766	0.2521	0.0172	0.1285	-0.0096	0.0136	0.1253	0.0191	0.1732	48.7163	38.8164	17.6365
10	4.91	2.1568	-0.1927	1.557	-0.0312	0.3446	-0.0207	-0.0893	0.0602	-0.0479	0.0056	-0.0298	0.0224	0.008	0.0273	0.1267	-0.0082	-0.015	0.0914	0.0126	0.1286	31.5863	23.2402	19.7341
11	1.1854	0.1836	0.4648	0.8398	0.4935	2.8533	-0.0005	-0.1136	-0.0598	0.0458	-0.0071	-0.0113	0.183	0.0465	0.011	0.0977	-0.0188	-0.0014	0.0806	0.0233	0.1072	28.2891	5.7647	34.8975
12	0.8331	-0.725	-1.0029	1.718	2.074	4.0361	-0.1026	-0.2115	0.0602	0.113	-0.0159	0.1154	0.0003	-0.0777	0.0807	0.0931	-0.009	-0.0056	0.1705	-0.0198	0.1417	21.4067	24.274	45.458
13	0.762	-0.157	0.0923	0.7579	-0.1816	2.0909	0.026	0.0874	-0.0397	-0.0102	-0.0087	0.0506	0.1017	-0.0908	-0.0197	0.0832	0.0139	-0.0005	0.0928	-0.0038	0.1048	8.9047	9.999	-35.0019
14	1.6648	0.0594	-0.3529	3.7183	-1.5236	3.6581	-0.0536	0.1187	0.1924	0.0907	0.2178	0.1766	-0.4537	-0.3715	-0.1071	0.1499	0.0424	-0.0132	0.1971	0.0552	0.1207	12.69	34.1302	-48.6603
15	0.6117	0.2744	-0.6632	1.3448	-1.8554	3.8656	-0.1016	0.1529	0.0211	-0.2077	-0.102	-0.1542	0.2466	0.2522	0.1751	0.1032	-0.0026	0.0018	0.1574	0.008	0.139	18.3546	24.2968	-46.8889
16	3.5489	0.6393	-1.9005	1.1851	-1.1706	2.9455	0.0097	-0.3574	0.1456	0.2712	-0.2748	-0.263	-0.3871	0.9503	0.0872	0.0902	-0.0715	-0.0346	0.3497	0.0827	0.1565	25.7711	27.881	-37.4729

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 33 through 68 )	A	33 - 68
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 143 )	A	69 - 143
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 243 )	A	144 - 243
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 244 through 319 )	A	244 - 319
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 33 through 95 )	B	33 - 95
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 96 through 143 )	B	96 - 143
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 144 through 190 )	B	144 - 190
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 191 through 243 )	B	191 - 243
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 244 through 274 )	B	244 - 274
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 275 through 319 )	B	275 - 319
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 33 through 126 )	C	33 - 126
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 127 through 319 )	C	127 - 319
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 33 through 143 )	D	33 - 143
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 144 through 190 )	D	144 - 190
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 191 through 300 )	D	191 - 300
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 301 through 319 )	D	301 - 319

-
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