PDB-7x0k: Crystal structure of sugar binding protein CbpB complexed wtih ce...

ID or keywords:

Entry

Database: PDB / ID: 7x0k

Title

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

Components

CpbB

Keywords

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

Function / homology

beta-cellotriose

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	Nov 20, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7x0k.cif.gz	474.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7x0k_validation.pdf.gz	963.5 KB	Display	wwPDB validaton report
Full document	7x0k_full_validation.pdf.gz	965.5 KB	Display
Data in XML	7x0k_validation.xml.gz	38.1 KB	Display
Data in CIF	7x0k_validation.cif.gz	59.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0k ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0k	HTTPS FTP

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Related structure data

Related structure data	7x0gC 7x0hC 7x0iC 7x0jC 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: CpbB

B: CpbB

hetero molecules

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

1

A: CpbB

hetero molecules

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

2

B: CpbB

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.440, 44.150, 113.060
Angle α, β, γ (deg.)	90.000, 103.980, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

CpbB

Mass: 45855.402 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-(1-4)-beta-D-glucopyranose

Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose

Descriptor	Type	Program
DGlcpb1-4DGlcpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}	LINUCS	PDB-CARE

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 943 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

Y

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Experiment

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

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Sample preparation

Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M Ammonium phosphate monobasic, pH 4.6, 22% 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: May 6, 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→40.958 Å / Num. obs: 136991 / % possible obs: 95.6 % / Redundancy: 3.485 % / B_iso Wilson estimate: 17.8 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.114 / R_rim(I) all: 0.133 / Χ²: 1.099 / Net I/σ(I): 6.88

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	3.497	0.809	1.54	35291	10539	10092	0.603	0.95	95.8
1.74-1.79	3.368	0.676	1.79	33366	10388	9906	0.675	0.798	95.4
1.79-1.84	3.275	0.544	2.17	31307	10075	9560	0.734	0.648	94.9
1.84-1.9	3.553	0.44	2.89	33232	9716	9354	0.826	0.516	96.3
1.9-1.96	3.59	0.352	3.59	32783	9489	9132	0.893	0.411	96.2
1.96-2.03	3.502	0.28	4.31	30824	9132	8803	0.924	0.329	96.4
2.03-2.11	3.445	0.224	5.22	29439	8921	8546	0.945	0.263	95.8
2.11-2.19	3.258	0.188	5.85	25553	8426	7843	0.959	0.223	93.1
2.19-2.29	3.538	0.166	6.9	28032	8191	7924	0.967	0.195	96.7
2.29-2.4	3.566	0.152	7.45	26732	7766	7497	0.974	0.178	96.5
2.4-2.53	3.545	0.128	8.51	25259	7383	7125	0.979	0.15	96.5
2.53-2.69	3.519	0.115	9.28	23666	7032	6725	0.982	0.136	95.6
2.69-2.87	3.351	0.097	10.23	20549	6609	6132	0.984	0.116	92.8
2.87-3.1	3.622	0.088	11.93	21561	6118	5953	0.988	0.103	97.3
3.1-3.4	3.556	0.078	13.34	19449	5663	5470	0.99	0.091	96.6
3.4-3.8	3.543	0.073	14.5	17034	5074	4808	0.989	0.085	94.8
3.8-4.39	3.422	0.067	14.97	14269	4512	4170	0.99	0.078	92.4
4.39-5.38	3.681	0.067	15.97	13565	3790	3685	0.991	0.078	97.2
5.38-7.6	3.635	0.072	15.89	10014	2940	2755	0.989	0.084	93.7
7.6-40.958	3.617	0.073	16.96	5451	1597	1507	0.989	0.086	94.4

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 1.7→40.958 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2156	3852	2.81 %
R_work	0.1796	133139	-
obs	0.1806	136991	95.58 %

Solvent computation

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

Displacement parameters

B_iso max: 72.61 Å² / B_iso mean: 21.8061 Å² / B_iso min: 6.17 Å²

Refinement step

Cycle: final / Resolution: 1.7→40.958 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6293	0	132	943	7368
B_iso mean	-	-	18.98	29.32	-
Num. residues	-	-	-	-	813

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 (%)
1.7-1.7207	0.2918	134	0.2685	4666	96
1.7207-1.7425	0.3156	128	0.2601	4796	96
1.7425-1.7655	0.3284	157	0.2637	4772	96
1.7655-1.7896	0.3085	126	0.2507	4726	95
1.7896-1.8152	0.2684	150	0.2434	4633	94
1.8152-1.8423	0.2811	131	0.2354	4885	96
1.8423-1.8711	0.2556	141	0.2163	4732	96
1.8711-1.9018	0.224	154	0.2088	4744	96
1.9018-1.9346	0.2394	131	0.2029	4861	96
1.9346-1.9697	0.2538	134	0.1986	4687	96
1.9697-2.0076	0.2586	135	0.2018	4883	97
2.0076-2.0486	0.227	124	0.1862	4788	97
2.0486-2.0931	0.2326	159	0.1828	4779	96
2.0931-2.1418	0.2424	131	0.1806	4674	95
2.1418-2.1954	0.2344	127	0.1853	4588	92
2.1954-2.2547	0.2116	135	0.1716	4801	97
2.2547-2.3211	0.2195	138	0.1722	4900	97
2.3211-2.396	0.1913	139	0.1713	4749	96
2.396-2.4816	0.2256	132	0.1682	4806	96
2.4816-2.581	0.2215	147	0.1689	4838	97
2.581-2.6984	0.2099	149	0.1728	4659	95
2.6984-2.8406	0.2436	129	0.1781	4605	92
2.8406-3.0186	0.2053	147	0.182	4831	97
3.0186-3.2515	0.2169	122	0.1687	4838	97
3.2515-3.5786	0.1801	149	0.1583	4796	96
3.5786-4.096	0.1533	129	0.1482	4602	92
4.096-5.1589	0.195	140	0.1477	4779	97
5.1589-40.9	0.1945	134	0.1882	4721	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	2.4767	0.1252	-1.9075	1.3146	0.7675	2.6334	-0.268	0.2107	-0.2596	0.0392	-0.2002	-0.0507	0.4602	0.0336	0.429	0.1653	0.0135	0.0174	0.1064	0.0032	0.1958	-15.0934	6.4248	37.4875
2	1.1121	0.3806	0.2908	1.6379	1.1586	1.9713	0.0382	0.1899	-0.1552	-0.2056	0.0605	-0.0259	0.0153	0.027	-0.1141	0.2101	-0.0023	0.0052	0.1891	-0.0163	0.1711	20.2234	28.111	9.0598
3	1.9014	0.4009	-0.0023	2.7166	-0.0964	2.4258	-0.0389	0.1953	0.1031	-0.1782	0.0944	0.1988	-0.2417	-0.1766	-0.0442	0.1405	0.0133	-0.0007	0.1631	0.0164	0.1434	5.896	32.0777	12.9894
4	0.4415	0.2219	0.1366	1.4075	-0.8864	2.0408	0.0495	0.1161	0.0002	-0.135	-0.0303	0.1065	0.1164	0.0762	-0.0505	0.0856	-0	0.0098	0.1145	-0.0359	0.1407	9.7319	19.3775	24.3632
5	0.896	0.1932	0.0345	1.9101	-0.3304	1.5815	-0.0431	-0.0697	-0.1698	0.1058	-0.0043	-0.3725	0.1751	0.2301	0.0541	0.1218	0.032	-0.0005	0.1649	-0.0039	0.186	17.0063	11.9727	41.8983
6	1.2055	-0.1087	-0.4177	0.9054	0.1806	0.7849	0.0278	0.0172	-0.0241	-0.0468	-0.0414	-0.0924	0.0765	0.0827	0.0056	0.0984	0.0021	0.0052	0.1158	0.004	0.1203	13.8095	19.4053	35.1972
7	1.3956	0.1349	0.0885	2.7255	-0.9169	2.1362	0.0178	0.1789	0.0785	-0.3426	0.0827	0.0781	-0.0553	0.0391	-0.0839	0.1512	-0.0164	0.0067	0.1105	-0.0039	0.095	11.7482	25.3513	6.7747
8	0.4383	-0.1289	-0.0715	0.039	0.0563	1.004	-0.0157	0.0124	-0.0339	-0.0176	0.0453	-0.0361	0.0222	0.0791	-0.0292	0.1204	0.0048	0.0096	0.1376	0.004	0.1705	8.977	20.729	25.997
9	2.5389	-1.6852	0.5008	2.0567	-1.4079	1.8217	0.1336	-0.0154	0.2347	-0.1783	-0.0208	-0.1487	0.0582	0.0944	-0.0549	0.2071	-0.0406	0.0086	0.1956	-0.0611	0.208	10.1439	35.9912	45.1815
10	1.7997	-0.1001	0.1221	1.2342	-0.1352	1.3239	0.0625	0.2061	0.0613	-0.1732	-0.0473	0.0392	0.0784	0.0106	-0.0155	0.1497	0.0048	-0.0003	0.138	-0.0047	0.0866	-28.2162	25.979	13.5872
11	0.4018	0.0984	0.1732	0.5685	0.4298	1.9498	0.0221	0.0898	0.0304	-0.115	0.0149	0.0128	-0.0058	0.0731	-0.0637	0.0789	0.0047	0.0054	0.0706	0.0203	0.1413	-21.1628	30.7191	29.8298
12	2.0487	0.5379	0.2205	1.0852	0.6248	1.7571	0.0562	0.0496	0.0341	0.0384	-0.0034	0.0408	-0.0157	-0.1031	-0.0593	0.0868	0.0147	0.0082	0.0726	0.0242	0.1048	-24.749	31.0378	50.2289
13	1.0903	-0.6749	-0.074	0.8474	0.1362	0.3383	0.0464	0.0304	0.0297	-0.0343	-0.0404	0.0451	-0.0528	-0.0244	-0.0058	0.1248	-0.0042	-0.0013	0.0951	-0.0009	0.1276	-23.3331	25.9793	39.8703
14	0.9866	-0.0509	-0.0015	1.8866	1.1142	1.7966	0.0274	0.2214	0.0527	-0.3257	-0.0539	0.0077	-0.166	-0.0153	0.0287	0.1405	0.0142	-0.0244	0.1357	0.0147	0.0845	-26.3627	31.7182	11.4496
15	0.1398	-0.1248	0.213	0.2409	-0.5199	0.9031	-0.0188	0.025	0.0282	0.0041	0.0377	0.0376	-0.0064	-0.0725	-0.0195	0.1482	-0.0039	0.0021	0.1165	-0.0005	0.1601	-21.29	26.4322	32.9207

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 436 through 455 )	B	436 - 455
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 219 )	A	178 - 219
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 220 through 332 )	A	220 - 332
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 333 through 369 )	A	333 - 369
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 370 through 427 )	A	370 - 427
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 428 through 454 )	A	428 - 454
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 147 )	B	49 - 147
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 148 through 177 )	B	148 - 177
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 178 through 218 )	B	178 - 218
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 219 through 332 )	B	219 - 332
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 333 through 369 )	B	333 - 369
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 370 through 435 )	B	370 - 435

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