PDB-7x0r: Crystal structure of substrate binding protein Lbp complexed wtih...

ID or keywords:

Entry

Database: PDB / ID: 7x0r

Title

Crystal structure of substrate binding protein Lbp complexed wtih guanosine from Clostridium thermocellum

Components

Lbp

Keywords

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

Function / homology

GUANOSINE

Function and homology information

Biological species

Acetivibrio thermocellus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.47 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 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x0r.cif.gz	352.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7x0r.ent.gz	287.8 KB	Display	PDB format
PDBx/mmJSON format	7x0r.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7x0r_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7x0r_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7x0r_validation.xml.gz	28.5 KB	Display
Data in CIF	7x0r_validation.cif.gz	43 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0r ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0r	HTTPS FTP

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Related structure data

Related structure data	7x0gC 7x0hC 7x0iC 7x0jC 7x0kC 7x0lC 7x0mC 7x0nC 7x0oC 7x0pC 7x0qC 2fqxS S: Starting model for refinement 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: Lbp

B: Lbp

hetero molecules

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

1

A: Lbp

hetero molecules

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

2

B: Lbp

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.830, 62.090, 81.300
Angle α, β, γ (deg.)	90.000, 101.700, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lbp Mass: 35409.379 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: Chemical	ChemComp-GMP / GUANOSINE Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 529 / 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: 1.86 Å³/Da / Density % sol: 34.02 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M zinc acetate, 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: 0.9792 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 1.47→31.045 Å / Num. obs: 165622 / % possible obs: 94.4 % / Redundancy: 1.774 % / B_iso Wilson estimate: 14.76 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.046 / R_rim(I) all: 0.062 / Χ²: 1.068 / Net I/σ(I): 9.73 / Num. measured all: 293817 / Scaling rejects: 4

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
1.47-1.51	1.615	0.373	2.15	19111	12964	11830	0.756	0.508	91.3
1.51-1.55	1.801	0.3	2.83	21427	12744	11898	0.842	0.402	93.4
1.55-1.59	1.821	0.244	3.38	21188	12320	11634	0.882	0.328	94.4
1.59-1.64	1.806	0.198	3.97	20165	11870	11164	0.923	0.266	94.1
1.64-1.7	1.761	0.164	4.67	18945	11578	10759	0.946	0.221	92.9
1.7-1.76	1.818	0.138	5.59	19641	11277	10804	0.96	0.186	95.8
1.76-1.82	1.796	0.115	6.67	18522	10776	10312	0.969	0.155	95.7
1.82-1.9	1.728	0.086	8.33	17165	10418	9934	0.983	0.117	95.4
1.9-1.98	1.785	0.068	10.11	16851	9966	9441	0.988	0.092	94.7
1.98-2.08	1.816	0.057	11.86	16531	9584	9101	0.991	0.077	95
2.08-2.19	1.794	0.049	13.52	15210	9033	8477	0.992	0.067	93.8
2.19-2.32	1.74	0.044	14.55	13963	8576	8023	0.993	0.06	93.6
2.32-2.48	1.809	0.041	15.54	14066	8087	7775	0.994	0.057	96.1
2.48-2.68	1.787	0.039	16.56	12764	7493	7143	0.994	0.054	95.3
2.68-2.94	1.718	0.036	17.43	11264	6908	6558	0.994	0.05	94.9
2.94-3.29	1.833	0.034	19.44	10895	6240	5943	0.995	0.046	95.2
3.29-3.8	1.765	0.031	20.06	9158	5502	5190	0.996	0.043	94.3
3.8-4.65	1.78	0.031	20.92	7854	4645	4413	0.995	0.043	95
4.65-6.57	1.72	0.031	20.04	5827	3571	3388	0.995	0.044	94.9
6.57-31.045	1.782	0.034	20.61	3270	1976	1835	0.994	0.048	92.9

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
Aimless	0.7.4	data scaling
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FQX

2fqx

Resolution: 1.47→31.045 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1736	3743	2.26 %
R_work	0.1565	161855	-
obs	0.1569	165598	94.37 %

Solvent computation

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

Displacement parameters

B_iso max: 70.46 Å² / B_iso mean: 21.1172 Å² / B_iso min: 7.83 Å²

Refinement step

Cycle: final / Resolution: 1.47→31.045 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4617	0	48	529	5194
B_iso mean	-	-	14.02	32.72	-
Num. residues	-	-	-	-	624

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 (%)
1.47-1.4885	0.2419	133	0.2439	5766	91
1.4885-1.5081	0.2265	133	0.228	5799	91
1.5081-1.5288	0.2179	138	0.2173	5928	93
1.5288-1.5506	0.2218	140	0.2064	6016	94
1.5506-1.5738	0.194	133	0.2014	5987	95
1.5738-1.5984	0.2428	137	0.1945	6021	95
1.5984-1.6246	0.1991	140	0.1887	5945	94
1.6246-1.6526	0.2259	137	0.1863	5965	94
1.6526-1.6826	0.2326	136	0.1817	5923	92
1.6826-1.715	0.1772	139	0.1793	5913	95
1.715-1.75	0.2071	141	0.1791	6102	96
1.75-1.788	0.1937	142	0.1736	6101	96
1.788-1.8296	0.1969	140	0.1694	6121	96
1.8296-1.8754	0.1788	135	0.1564	5974	95
1.8754-1.9261	0.1603	138	0.1576	6072	95
1.9261-1.9827	0.1829	142	0.1492	6005	95
1.9827-2.0467	0.1753	139	0.1428	6072	95
2.0467-2.1199	0.1339	142	0.1343	5943	94
2.1199-2.2047	0.1756	138	0.1339	5990	94
2.2047-2.305	0.1617	137	0.1339	5911	93
2.305-2.4265	0.142	139	0.136	6115	96
2.4265-2.5785	0.1419	142	0.141	6085	96
2.5785-2.7774	0.1679	143	0.1418	6007	95
2.7774-3.0567	0.192	135	0.1413	6025	95
3.0567-3.4985	0.1424	144	0.1384	6038	95
3.4985-4.4058	0.1524	140	0.1367	6028	95
4.4058-31.04	0.1943	140	0.1961	6003	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	6.2789	1.9137	0.8414	2.4017	1.8953	1.614	-0.043	-0.4302	0.3974	0.0237	-0.0008	0.0201	-0.1473	-0.256	0.0635	0.1373	-0.0061	0.02	0.142	-0.0037	0.0939	11.4054	-2.6061	34.5532
2	4.3507	-3.1669	1.2239	6.5848	-1.9887	3.4497	0.1454	-0.0934	-0.1578	-0.0002	0.0139	0.1745	0.1612	-0.1549	-0.1222	0.089	-0.0097	0.0326	0.0953	0.0073	0.0668	11.8233	-8.029	35.7425
3	5.1512	-0.3759	0.6482	6.4873	2.2253	5.3389	-0.0941	-0.0199	0.1509	0.2494	0.1595	-0.1993	-0.1378	-0.0286	-0.0699	0.1076	-0.0122	0.0013	0.0794	0.0167	0.1067	19.4469	2.8811	37.07
4	3.2641	0.4586	2.1726	2.4905	0.9378	3.2565	-0.07	0.201	0.1824	-0.1158	0.0642	-0.3298	-0.2097	0.2319	0.0067	0.1101	-0.0162	0.0415	0.134	0.0311	0.1612	22.644	2.4199	26.0612
5	2.2842	0.0112	1.3369	1.9079	0.7326	2.9528	-0.013	0.0798	0.0705	-0.0895	-0.0205	0.0193	-0.069	0.0567	0.0368	0.0938	0.0101	0.0126	0.0759	0.0203	0.0572	-0.7794	0.2022	11.3833
6	1.8593	-0.5278	1.2299	0.978	-0.2292	1.1765	0.0422	-0.0393	-0.0908	-0.0266	0.0099	0.0473	0.0858	-0.0707	-0.0541	0.1171	-0	0.0213	0.1065	0.0082	0.0869	1.0939	-6.776	21.5304
7	3.1004	1.1633	0.9622	3.3961	0.0532	1.6307	0.1905	0.5244	-0.2645	-0.9783	-0.2666	-0.0401	0.4473	0.4548	-0.0244	0.3756	0.0907	-0.0296	0.1996	-0.0661	0.177	5.1622	-13.2316	5.3321
8	2.9961	0.8854	-1.9188	8.3624	3.6257	3.5507	0.0028	0.2785	0.3328	-0.4726	0.0005	-0.1003	-0.4915	0.0108	-0.0162	0.1751	-0.0037	-0.0047	0.2028	0.044	0.1337	4.5829	6.9279	4.0669
9	4.9135	-1.5455	1.0446	1.2291	-1.368	1.8212	-0.0862	0.6305	0.0366	-0.0534	0.1233	-0.0176	-0.15	0.3647	0.0297	0.0983	0.0004	0.0154	0.1334	-0.0041	0.0698	-3.0795	-3.1479	44.4567
10	3.0881	2.5696	1.2532	8.292	3.0847	3.0045	0.0323	0.1542	-0.14	-0.0971	0.083	-0.092	0.1027	0.1313	-0.0899	0.0701	0.0007	0.034	0.1024	-0.0041	0.0695	-1.7729	-7.7598	43.688
11	4.6711	1.8341	1.2093	6.6704	-1.1032	2.8648	-0.0446	0.0616	0.157	-0.248	0.0224	0.1702	-0.1201	0.0242	0.009	0.0879	0.0178	0.0213	0.0836	-0.0111	0.09	-10.4384	2.7079	43.5739
12	3.81	-0.3165	2.0489	1.5426	-0.028	2.2911	-0.0716	-0.1589	0.137	0.0118	0.0044	0.1153	-0.1486	-0.1325	0.0711	0.0915	0.0069	0.0256	0.1199	-0.0124	0.1114	-12.9268	1.0021	54.8562
13	1.7586	-0.3031	0.9767	1.6142	-0.6492	2.0006	-0.0561	-0.0927	0.0544	0.078	0.0374	-0.033	-0.068	0.028	0.0223	0.0908	0.001	0.0127	0.1028	-0.0245	0.0701	11.1838	-0.0674	68.1726
14	1.3635	0.1926	0.5616	0.577	0.0647	0.8949	-0.0073	0.0331	-0.0164	0.0036	0.0257	-0.0227	0.0162	0.0871	-0.0228	0.1004	0.0054	0.0215	0.1018	-0.0066	0.0869	9.5148	-6.3753	57.547
15	3.2657	-1.4895	-0.4253	4.9763	0.0096	1.4723	-0.2056	-0.3312	-0.4388	0.3201	0.2088	0.3292	0.2349	-0.015	0.016	0.1949	0.018	0.0264	0.1622	0.029	0.1096	6.9389	-14.5935	73.2418
16	8.2923	-0.629	-0.4308	6.331	-2.622	4.2612	0.0124	-0.3353	0.2265	0.3738	-0.1018	0.2103	-0.1252	-0.0615	0.0664	0.1364	-0.0069	0.0207	0.1436	-0.053	0.0888	5.5062	5.4842	76.1962

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 45 through 61 )	A	45 - 61
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 62 through 88 )	A	62 - 88
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 89 through 111 )	A	89 - 111
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 112 through 149 )	A	112 - 149
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 150 through 211 )	A	150 - 211
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 212 through 315 )	A	212 - 315
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 316 through 339 )	A	316 - 339
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 340 through 355 )	A	340 - 355
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 61 )	B	43 - 61
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 62 through 88 )	B	62 - 88
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 89 through 111 )	B	89 - 111
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 112 through 149 )	B	112 - 149
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 150 through 211 )	B	150 - 211
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 212 through 315 )	B	212 - 315
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 316 through 339 )	B	316 - 339
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 340 through 355 )	B	340 - 355

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