PDB-5fq7: Crystal structure of the SusCD complex BT2261-2264 from Bacteroid...

ID or keywords:

Entry

Database: PDB / ID: 5fq7

Title

Crystal structure of the SusCD complex BT2261-2264 from Bacteroides thetaiotaomicron

Components

BT_2261
BT_2262
BT_2263
BT_2264
PEPTIDE

Keywords

MEMBRANE PROTEIN / SUGAR BINDING PROTEIN / OUTER MEMBRANE NUTRIENT IMPORTER SUSCD COMPLEX

Function / homology

Function and homology information

cell outer membrane / metal ion binding
Similarity search - Function

Biological species

BACTEROIDES THETAIOTAOMICRON (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

Glenwright, A.J. / Pothula, K.R. / Chorev, D.S. / Basle, A. / Robinson, C.V. / Kleinekathoefer, U. / Bolam, D.N. / van den Berg, B.

Citation

Journal: Nature / Year: 2017
Title: Structural basis for nutrient acquisition by dominant members of the human gut microbiota.
Authors: Glenwright, A.J. / Pothula, K.R. / Bhamidimarri, S.P. / Chorev, D.S. / Basle, A. / Firbank, S.J. / Zheng, H. / Robinson, C.V. / Winterhalter, M. / Kleinekathofer, U. / Bolam, D.N. / van den Berg, B.

History

Deposition	Dec 7, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 21, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2017	Group: Database references
Revision 1.2	Jan 25, 2017	Group: Database references
Revision 1.3	Feb 1, 2017	Group: Database references
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fq7.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb5fq7.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	5fq7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fq7_validation.pdf.gz	519.8 KB	Display	wwPDB validaton report
Full document	5fq7_full_validation.pdf.gz	583.7 KB	Display
Data in XML	5fq7_validation.xml.gz	113.4 KB	Display
Data in CIF	5fq7_validation.cif.gz	155.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fq/5fq7 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fq7	HTTPS FTP

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Related structure data

Related structure data	5fq3SC 5fq4SC 5fq6C 5fq8C 5lx8C 5t3rC 5t4yC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	30296 30297 5fq8-d 4933 6w6v-d 5fq6-2 11287 4795 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: BT_2263

B: BT_2264

C: BT_2263

D: BT_2264

E: BT_2261

F: BT_2261

G: BT_2262

H: BT_2262

I: PEPTIDE

P: PEPTIDE

hetero molecules

405 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	123.591, 180.159, 245.747
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 4 types, 8 molecules ACBDEFGH

#1: Protein	BT_2263 Mass: 53145.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H6
#2: Protein	BT_2264 Mass: 108954.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TONB DEPENDENT TRANSPORTER / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H5
#3: Protein	BT_2261 Mass: 16428.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H8
#4: Protein	BT_2262 Mass: 23399.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUTER MEMBRANE LIPOPROTEIN / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria) / References: UniProt: Q8A5H7

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Protein/peptide , 1 types, 2 molecules IP

#5: Protein/peptide	PEPTIDE Mass: 588.533 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BACTEROIDES THETAIOTAOMICRON (bacteria)

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Non-polymers , 2 types, 8 molecules

#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na

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Details

Sequence details	IDENTITY OF PEPTIDE IS UNKNOWN. FITTED SEQUENCE PROVIDES A REASONABLE FIT TO THE DENSITY. PROBABLY ...IDENTITY OF PEPTIDE IS UNKNOWN. FITTED SEQUENCE PROVIDES A REASONABLE FIT TO THE DENSITY. PROBABLY AN ENSEMBLE OF PEPTIDES IS BOUND.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.4 Å³/Da / Density % sol: 64 % / Description: ORTHORHOMBIC CRYSTAL FORM
Crystal grow	Details: 0.2 M MAGNESIUM FORMATE DIHYDRATE 0.05 M TRIS PH 8 18-22% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
Detector	Type: DECTRIS PIXEL / Detector: PIXEL / Date: Jan 31, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 3.4→49.45 Å / Num. obs: 76187 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / R_merge(I) obs: 0.17 / Net I/σ(I): 10.3
Reflection shell	Resolution: 3.4→3.47 Å / Redundancy: 7.6 % / R_merge(I) obs: 1.03 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 5FQ4, 5FQ3

5fq4

5fq3

Resolution: 3.4→48.432 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 24.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2554	7447	9.8 %
R_work	0.2006	-	-
obs	0.206	76084	99.96 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.4→48.432 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25878	0	8	0	25886

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	26491
X-RAY DIFFRACTION	f_angle_d	1.175	35972
X-RAY DIFFRACTION	f_dihedral_angle_d	12.938	15482
X-RAY DIFFRACTION	f_chiral_restr	0.063	3830
X-RAY DIFFRACTION	f_plane_restr	0.007	4730

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.4-3.4386	0.3271	266	0.273	2233	X-RAY DIFFRACTION	100
3.4386-3.4791	0.3032	251	0.2677	2245	X-RAY DIFFRACTION	100
3.4791-3.5215	0.3161	250	0.271	2280	X-RAY DIFFRACTION	100
3.5215-3.5661	0.299	249	0.2467	2238	X-RAY DIFFRACTION	100
3.5661-3.613	0.2726	241	0.2322	2257	X-RAY DIFFRACTION	100
3.613-3.6624	0.3054	245	0.2406	2281	X-RAY DIFFRACTION	100
3.6624-3.7147	0.3057	238	0.2324	2261	X-RAY DIFFRACTION	100
3.7147-3.7702	0.2788	251	0.2152	2283	X-RAY DIFFRACTION	100
3.7702-3.8291	0.3135	224	0.2201	2268	X-RAY DIFFRACTION	100
3.8291-3.8918	0.2987	224	0.2161	2283	X-RAY DIFFRACTION	100
3.8918-3.9589	0.2558	261	0.213	2248	X-RAY DIFFRACTION	100
3.9589-4.0308	0.2829	237	0.214	2262	X-RAY DIFFRACTION	100
4.0308-4.1083	0.2546	250	0.2031	2294	X-RAY DIFFRACTION	100
4.1083-4.1921	0.2465	257	0.1954	2244	X-RAY DIFFRACTION	100
4.1921-4.2832	0.2397	257	0.1966	2284	X-RAY DIFFRACTION	100
4.2832-4.3828	0.2393	261	0.179	2241	X-RAY DIFFRACTION	100
4.3828-4.4924	0.229	254	0.1644	2267	X-RAY DIFFRACTION	100
4.4924-4.6137	0.2206	265	0.1676	2265	X-RAY DIFFRACTION	100
4.6137-4.7494	0.2115	255	0.1594	2292	X-RAY DIFFRACTION	100
4.7494-4.9025	0.2118	236	0.1576	2275	X-RAY DIFFRACTION	100
4.9025-5.0776	0.2213	233	0.1651	2309	X-RAY DIFFRACTION	100
5.0776-5.2806	0.2244	274	0.167	2253	X-RAY DIFFRACTION	100
5.2806-5.5206	0.2186	236	0.1883	2308	X-RAY DIFFRACTION	100
5.5206-5.8113	0.2347	255	0.1887	2298	X-RAY DIFFRACTION	100
5.8113-6.1747	0.2559	249	0.1833	2314	X-RAY DIFFRACTION	100
6.1747-6.6503	0.2595	215	0.1856	2348	X-RAY DIFFRACTION	100
6.6503-7.3175	0.2605	263	0.188	2321	X-RAY DIFFRACTION	100
7.3175-8.3716	0.2186	214	0.1764	2370	X-RAY DIFFRACTION	100
8.3716-10.5295	0.2088	260	0.1753	2370	X-RAY DIFFRACTION	100
10.5295-48.4371	0.3285	276	0.2876	2445	X-RAY DIFFRACTION	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	1.1757	-0.2902	0.235	0.8254	-0.3526	1.2718	0.1362	-0.3053	-0.0303	0.3347	-0.0158	-0.111	0.0549	0.0739	-0.1328	0.7347	-0.1147	-0.0793	0.5815	-0.0637	0.6268	33.6123	7.7707	-6.6392
2	1.1219	-0.1152	0.1877	0.7614	-0.1035	0.7767	0.1591	0.3949	-0.0865	-0.1958	-0.0634	-0.2248	0.0884	0.2641	-0.1035	0.6065	0.047	0.0103	0.6829	-0.1004	0.629	40.8768	4.6429	-51.0412
3	1.4286	-0.1424	-0.2621	1.3606	0.1163	0.9372	0.1563	-0.0877	-0.6107	0.3791	0.0319	-0.5996	0.5879	0.726	-0.1453	0.9644	0.1695	-0.2866	1	-0.0188	1.2508	70.5078	-27.4462	-15.9038
4	1.904	0.229	-0.7001	3.486	-1.6001	3.083	0.0005	-0.2646	-0.6216	0.6478	0.151	0.2315	0.2603	-0.5251	-0.1806	1.0638	-0.0449	-0.1492	0.9407	-0.042	1.0597	36.0485	-46.1029	-12.3784
5	4.3801	-1.1105	2.6541	9.1714	-2.7445	6.5222	0.0987	-0.0578	-0.2484	-1.0679	0.0024	1.4313	-0.3685	-0.2037	-0.1129	0.6174	0.1846	-0.0545	0.7794	-0.235	0.7148	40.1066	-2.4408	-27.6149
6	1.7367	-0.6472	-0.0437	1.1487	0.1287	1.2319	0.0975	-0.3286	-0.3754	0.1456	0.0734	0.3313	0.1983	-0.223	-0.1685	0.611	-0.0867	-0.0428	0.6536	0.091	0.6995	-17.7565	-4.2267	-18.1232
7	0.8757	-0.0202	0.0176	0.4419	-0.157	0.7479	0.1185	0.3688	-0.0669	-0.2694	-0.0162	0.1303	0.0373	-0.0543	-0.1021	0.6655	0.0585	-0.0613	0.6584	-0.0393	0.5775	-9.0298	11.9416	-59.3465
8	1.1255	0.0364	-0.0066	1.005	-0.0271	0.7706	0.2977	0.2784	0.142	-0.0997	-0.0701	0.3773	-0.2024	-0.4061	-0.1857	0.7322	0.1511	0.0192	1.0338	0.0019	0.9372	-51.4076	33.3821	-29.3946
9	3.0388	-1.7579	-4.0389	1.679	3.5726	9.6987	-0.5236	-0.6652	0.1001	0.4279	0.2829	-0.0162	0.7595	1.0069	0.3294	0.8703	0.0637	0.1032	0.8093	-0.0002	0.9176	-22.0493	49.8754	-7.5798
10	5.8394	1.237	-1.1767	0.7839	-1.4191	2.8615	0.3567	0.2317	0.234	-0.7656	0.3799	-1.3091	-0.1285	0.6419	-0.6956	0.4929	0.2059	-0.0741	0.5933	0.0792	0.5649	-17.1286	11.9829	-36.2791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN 'A' AND RESID 1 THROUGH 480)
2	X-RAY DIFFRACTION	2	(CHAIN 'B' AND RESID 37 THROUGH 984)
3	X-RAY DIFFRACTION	3	(CHAIN 'F' AND RESID 4 THROUGH 148)
4	X-RAY DIFFRACTION	4	(CHAIN 'G' AND RESID 2 THROUGH 87)
5	X-RAY DIFFRACTION	5	(CHAIN 'P' AND RESID 1 THROUGH 10)
6	X-RAY DIFFRACTION	6	(CHAIN 'C' AND RESID 1 THROUGH 480)
7	X-RAY DIFFRACTION	7	(CHAIN 'D' AND RESID 38 THROUGH 984)
8	X-RAY DIFFRACTION	8	(CHAIN 'E' AND RESID 4 THROUGH 148)
9	X-RAY DIFFRACTION	9	(CHAIN 'H' AND RESID 2 THROUGH 90)
10	X-RAY DIFFRACTION	10	(CHAIN 'I' AND RESID 1 THROUGH 10)

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