PDB-8okv: lipoprotein BT2095 from Bacteroides thetaiotamicron bound to cyan...

ID or keywords:

Entry

Database: PDB / ID: 8okv

Title

lipoprotein BT2095 from Bacteroides thetaiotamicron bound to cyanocobalamin CnCbl

Components

Putative surface layer protein

Keywords

MEMBRANE PROTEIN / lipoprotein / membrane associated / beta propeller / B12 binding protein

Function / homology

Protein of unknown function DUF5074 / Domain of unknown function (DUF5074) / : / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / CYANOCOBALAMIN / Surface layer protein

Function and homology information

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Javier Abellon-Ruiz, J. / van den Berg, B. / Jana, K. / Kleinekathofer, U. / Silale, A. / Frey, A.M. / Basle, A. / Trost, M.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B uptake in gut Bacteroides.
Authors: Javier Abellon-Ruiz / Kalyanashis Jana / Augustinas Silale / Andrew M Frey / Arnaud Baslé / Matthias Trost / Ulrich Kleinekathöfer / Bert van den Berg /

Abstract: Vitamin B (cobalamin) is required for most human gut microbes, many of which are dependent on scavenging to obtain this vitamin. Since bacterial densities in the gut are extremely high, competition ...

History

Deposition	Mar 29, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8okv.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb8okv.ent.gz	855.8 KB	Display	PDB format
PDBx/mmJSON format	8okv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8okv_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8okv_full_validation.pdf.gz	2.2 MB	Display
Data in XML	8okv_validation.xml.gz	54.8 KB	Display
Data in CIF	8okv_validation.cif.gz	70.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/8okv ftp://data.pdbj.org/pub/pdb/validation_reports/ok/8okv	HTTPS FTP

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Related structure data

Related structure data	16114C 17574C 17575C 8blwC 8bmxC 8bmyC 8bmzC 8bn0C 8p97C 8p98C 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
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

B: Putative surface layer protein

A: Putative surface layer protein

C: Putative surface layer protein

D: Putative surface layer protein

hetero molecules

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

1

B: Putative surface layer protein

hetero molecules

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

2

A: Putative surface layer protein

hetero molecules

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

3

C: Putative surface layer protein

hetero molecules

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

4

D: Putative surface layer protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.770, 131.040, 179.380
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	B
3	2	B
4	2	B
5	3	B
6	3	B
7	4	B
8	4	B
9	5	B
10	5	B
11	6	B
12	6	B

NCS domain segments:

End auth comp-ID: TRP / End label comp-ID: TRP / Auth asym-ID: B / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	35 - 354	13 - 332
2	1	1	THR	THR	35 - 354	13 - 332
3	2	2	HIS	HIS	29 - 354	7 - 332
4	2	2	HIS	HIS	29 - 354	7 - 332
5	3	3	ALA	ALA	34 - 354	12 - 332
6	3	3	ALA	ALA	34 - 354	12 - 332
7	4	4	THR	THR	35 - 354	13 - 332
8	4	4	THR	THR	35 - 354	13 - 332
9	5	5	THR	THR	35 - 354	13 - 332
10	5	5	THR	THR	35 - 354	13 - 332
11	6	6	ALA	ALA	34 - 354	12 - 332
12	6	6	ALA	ALA	34 - 354	12 - 332

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Putative surface layer protein Mass: 38653.512 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_2095 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A5Z1
#2: Chemical	ChemComp-CNC / CYANOCOBALAMIN Mass: 1356.373 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆₃H₈₉CoN₁₄O₁₄P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.84 Å³/Da / Density % sol: 56.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Optimised from Index H8, 0.1MgFormate 15% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.6→74.7 Å / Num. obs: 54678 / % possible obs: 99.4 % / Redundancy: 13.2 % / CC_1/2: 0.99 / R_pim(I) all: 0.06 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.6→2.68 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4401 / CC_1/2: 0.66

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
xia2		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→74.123 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.905 / SU B: 40.204 / SU ML: 0.376 / Cross valid method: FREE R-VALUE / ESU R: 0.7 / ESU R Free: 0.338
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.276	2675	4.899 %
R_work	0.2182	51932	-
all	0.221	-	-
obs	-	54607	99.253 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 71.314 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.316 Å²	0 Å²	-0 Å²
2-	-	4.184 Å²	0 Å²
3-	-	-	-0.868 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→74.123 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10619	0	372	98	11089

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	11310
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.016	9952
X-RAY DIFFRACTION	r_angle_refined_deg	2.466	1.713	15478
X-RAY DIFFRACTION	r_angle_other_deg	0.896	1.606	23151
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.311	5	1296
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.158	5	50
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.463	10	1823
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.96	10	547
X-RAY DIFFRACTION	r_chiral_restr	0.132	0.2	1620
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	12788
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2429
X-RAY DIFFRACTION	r_nbd_refined	0.174	0.2	1745
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.166	0.2	9482
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	5338
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	5493
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.192	0.2	192
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.014	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	5.535	4.431	5196
X-RAY DIFFRACTION	r_mcbond_other	5.534	4.431	5196
X-RAY DIFFRACTION	r_mcangle_it	7.744	6.637	6488
X-RAY DIFFRACTION	r_mcangle_other	7.744	6.637	6489
X-RAY DIFFRACTION	r_scbond_it	5.969	4.867	6114
X-RAY DIFFRACTION	r_scbond_other	5.969	4.867	6114
X-RAY DIFFRACTION	r_scangle_it	8.54	7.217	8990
X-RAY DIFFRACTION	r_scangle_other	8.539	7.217	8991
X-RAY DIFFRACTION	r_lrange_it	10.071	53.232	11999
X-RAY DIFFRACTION	r_lrange_other	10.071	53.234	12000
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.111	0.05	10251
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.116	0.05	10475
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.117	0.05	10188
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.106	0.05	10309
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.094	0.05	10435
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.108	0.05	10244

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.11133	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.11133	0.05009
2	3	B	X-RAY DIFFRACTION	Local ncs	0.11552	0.05009
2	4	B	X-RAY DIFFRACTION	Local ncs	0.11552	0.05009
3	5	B	X-RAY DIFFRACTION	Local ncs	0.11727	0.05009
3	6	B	X-RAY DIFFRACTION	Local ncs	0.11727	0.05009
4	7	B	X-RAY DIFFRACTION	Local ncs	0.10593	0.05009
4	8	B	X-RAY DIFFRACTION	Local ncs	0.10593	0.05009
5	9	B	X-RAY DIFFRACTION	Local ncs	0.09405	0.05009
5	10	B	X-RAY DIFFRACTION	Local ncs	0.09405	0.05009
6	11	B	X-RAY DIFFRACTION	Local ncs	0.10819	0.05009
6	12	B	X-RAY DIFFRACTION	Local ncs	0.10819	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.6-2.667	0.415	203	0.389	3755	0.39	3988	0.855	0.882	99.2477	0.366
2.667-2.74	0.377	171	0.371	3681	0.371	3917	0.828	0.848	98.3406	0.338
2.74-2.82	0.39	167	0.306	3602	0.31	3791	0.89	0.929	99.4197	0.27
2.82-2.906	0.361	180	0.303	3500	0.306	3699	0.9	0.936	99.4863	0.262
2.906-3.002	0.303	160	0.275	3425	0.276	3603	0.935	0.947	99.5004	0.231
3.002-3.107	0.332	190	0.277	3271	0.281	3478	0.927	0.945	99.5112	0.237
3.107-3.224	0.312	165	0.26	3169	0.262	3347	0.922	0.955	99.6116	0.225
3.224-3.355	0.307	167	0.257	3064	0.259	3239	0.93	0.957	99.753	0.226
3.355-3.504	0.391	141	0.318	2914	0.322	3100	0.845	0.919	98.5484	0.281
3.504-3.675	0.325	135	0.268	2809	0.271	2977	0.908	0.95	98.8915	0.238
3.675-3.873	0.272	151	0.249	2652	0.25	2830	0.951	0.96	99.0459	0.22
3.873-4.107	0.325	130	0.241	2475	0.245	2700	0.892	0.951	96.4815	0.204
4.107-4.39	0.237	126	0.15	2416	0.154	2546	0.965	0.987	99.8429	0.134
4.39-4.74	0.188	125	0.129	2251	0.132	2378	0.982	0.99	99.9159	0.115
4.74-5.19	0.24	108	0.147	2078	0.151	2186	0.971	0.989	100	0.133
5.19-5.8	0.223	107	0.132	1887	0.137	1994	0.973	0.989	100	0.12
5.8-6.69	0.233	81	0.141	1700	0.145	1781	0.968	0.987	100	0.125
6.69-8.177	0.234	69	0.15	1452	0.154	1521	0.966	0.985	100	0.138
8.177-11.494	0.138	61	0.148	1139	0.148	1201	0.988	0.987	99.9167	0.144
11.494-74.123	0.256	38	0.256	692	0.256	740	0.957	0.948	98.6487	0.261

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	1.8763	0.3655	0.031	0.7562	-0.5006	2.3041	-0.0642	0.4201	-0.2444	-0.1824	0.1644	-0.1283	0.65	-0.029	-0.1002	0.4565	-0.0199	0.0254	0.2368	-0.0812	0.0615	22.6775	-19.5551	-8.092
2	2.4154	0.2348	0.7099	0.883	-0.8112	1.8188	-0.0335	-0.2341	0.1122	0.193	0.0527	0.0124	-0.1416	-0.5844	-0.0192	0.157	0.0376	-0.0065	0.3712	0.0182	0.0089	-3.4933	5.3277	-15.9654
3	0.8183	-0.0206	0.6611	0.664	-0.2358	3.9966	-0.2491	-0.221	0.2392	0.0821	-0.0787	-0.1231	-0.8746	-0.1973	0.3278	0.4253	0.0681	-0.1343	0.132	-0.0868	0.1186	22.9784	13.1036	28.4821
4	2.0282	-0.3372	-1.0562	1.0779	-0.6446	2.1658	-0.0871	0.5981	-0.2357	-0.1568	-0.0767	0.027	0.1801	-0.6392	0.1638	0.163	-0.06	0.0233	0.5414	-0.1435	0.0439	-2.7003	-9.3928	42.9334

Refinement TLS group

Selection: ALL

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