PDB-3v8u: The crystal structure of transferrin binding protein B (TbpB) fro...

ID or keywords:

Entry

Database: PDB / ID: 3v8u

Title

The crystal structure of transferrin binding protein B (TbpB) from Neisseria meningitidis serogroup B

Components

Transferrin binding-protein B

Keywords

TRANSPORT PROTEIN / transferrin binding protein / lipoprotein

Function / homology

Function and homology information

cellular response to iron ion / cell outer membrane / cell surface
Similarity search - Function

Biological species

Neisseria meningitidis serogroup B (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Noinaj, N. / Easley, N. / Buchanan, S.K.

Citation

Journal: Nature / Year: 2012
Title: Structural basis for iron piracy by pathogenic Neisseria.
Authors: Noinaj, N. / Easley, N.C. / Oke, M. / Mizuno, N. / Gumbart, J. / Boura, E. / Steere, A.N. / Zak, O. / Aisen, P. / Tajkhorshid, E. / Evans, R.W. / Gorringe, A.R. / Mason, A.B. / Steven, A.C. / Buchanan, S.K.

History

Deposition	Dec 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 29, 2012	Group: Database references
Revision 1.2	Apr 18, 2012	Group: Database references
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3v8u.cif.gz	435 KB	Display	PDBx/mmCIF format
PDB format	pdb3v8u.ent.gz	354 KB	Display	PDB format
PDBx/mmJSON format	3v8u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v8/3v8u ftp://data.pdbj.org/pub/pdb/validation_reports/v8/3v8u	HTTPS FTP

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Related structure data

Related structure data	3skpC 3v83C 3v89C 3v8xC C: citing same article (ref.)
Similar structure data	4qq1-3 6xsz-1 6xsz-4 6e7k-2 6m9t-d 3ap1-d 6xt1-2 6xt1-1 6xt1-4 5kdu-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Transferrin binding-protein B

B: Transferrin binding-protein B

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

1

A: Transferrin binding-protein B

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

2

B: Transferrin binding-protein B

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

Unit cell

Length a, b, c (Å)	75.030, 82.133, 111.314
Angle α, β, γ (deg.)	90.00, 106.07, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'A' and (resseq 37:106 or resseq 121:350 or resseq...
2	1	1	chain 'B' and (resseq 37:106 or resseq 121:350 or resseq...

#1: Protein	Transferrin binding-protein B Mass: 78484.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria) Gene: tbpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JPI9, UniProt: Q9K0V0*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H₂O
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	Density Matthews: 2.1 Å³/Da / Density % sol: 41.42 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.0 M NaCl and 2.0 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2010
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. all: 49472 / Num. obs: 49472 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / R_sym value: 0.12 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.7 / R_sym value: 0.54 / % possible all: 92.4

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Processing

Software

Name	Version	Classification
SERGUI		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→29.505 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.52 / σ(F): 0.06 / Phase error: 39.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3077	1961	4.04 %
R_work	0.253	-	-
obs	0.2552	48517	95.12 %
all	-	49472	-

Solvent computation

Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 29.162 Å² / k_sol: 0.302 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.2883 Å²	-0 Å²	-1.7235 Å²
2-	-	0.6031 Å²	0 Å²
3-	-	-	4.6853 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→29.505 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8219	0	0	147	8366

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	8394
X-RAY DIFFRACTION	f_angle_d	1.459	11322
X-RAY DIFFRACTION	f_dihedral_angle_d	18.056	3044
X-RAY DIFFRACTION	f_chiral_restr	0.1	1188
X-RAY DIFFRACTION	f_plane_restr	0.006	1492

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	4102	X-RAY DIFFRACTION	POSITIONAL
1	2	B	4102	X-RAY DIFFRACTION	POSITIONAL	0.06

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 (%)
2.4-2.46	0.5342	133	0.4682	3198	X-RAY DIFFRACTION	93
2.46-2.5265	0.4518	143	0.4194	3292	X-RAY DIFFRACTION	94
2.5265-2.6008	0.453	140	0.4011	3315	X-RAY DIFFRACTION	95
2.6008-2.6847	0.4161	132	0.3579	3304	X-RAY DIFFRACTION	95
2.6847-2.7806	0.3868	144	0.3263	3353	X-RAY DIFFRACTION	96
2.7806-2.8918	0.3256	140	0.2929	3360	X-RAY DIFFRACTION	97
2.8918-3.0233	0.3263	141	0.2682	3375	X-RAY DIFFRACTION	97
3.0233-3.1825	0.3136	141	0.2535	3409	X-RAY DIFFRACTION	98
3.1825-3.3816	0.3016	146	0.2519	3418	X-RAY DIFFRACTION	98
3.3816-3.6423	0.2869	123	0.253	2987	X-RAY DIFFRACTION	85
3.6423-4.008	0.3057	131	0.2334	2964	X-RAY DIFFRACTION	85
4.008-4.5861	0.2277	148	0.1803	3507	X-RAY DIFFRACTION	100
4.5861-5.7709	0.2628	145	0.1863	3514	X-RAY DIFFRACTION	100
5.7709-29.5077	0.2541	154	0.2048	3560	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	1.5611	0.7143	0.9475	2.5929	1.865	2.6547	0.0119	0.3827	0.0447	-0.2501	-0.0998	0.1541	-0.1395	-0.1919	0.0985	0.2235	-0.037	-0.0174	1.0261	0.1398	0.2427	-24.2291	5.304	-40.3125
2	2.4966	1.4581	1.6712	2.1743	0.6278	2.3905	0.1356	0.2812	-0.1513	-0.2211	-0.0564	0.0741	0.2078	-0.0134	-0.0397	0.263	0.0232	-0.0198	1.1041	-0.1372	0.2692	-22.7439	-11.3677	-40.7651
3	1.3552	0.3004	0.681	0.8612	0.4781	1.0698	0.0455	0.239	-0.0788	-0.1395	0.0591	0.1105	0.0151	-0.0236	-0.0195	0.1392	0.0285	-0.0642	0.8749	0.0494	0.1734	-30.6984	-4.8104	-37.9238
4	3.4175	-0.8859	1.888	0.9256	-1.1357	3.4982	-0.1938	-0.3744	0.324	0.0656	0.1038	0.1444	-0.1977	-0.3919	0.1585	0.3138	0.0333	-0.2037	0.7524	-0.028	0.4389	-30.0269	8.0824	-23.3384
5	0.4699	0.6878	-0.1995	3.8126	-0.2462	2.6142	-0.1128	-0.3461	-0.2318	-0.1044	0.1867	0.405	-0.0253	-0.5517	-0.0808	0.162	0.0809	0.0083	0.6112	0.045	0.1634	-32.6683	1.5972	-23.8749
6	1.3474	-0.3384	0.5606	0.9986	0.0009	1.5255	0.0479	0.135	0.0035	-0.0005	0.0269	-0.0158	-0.018	0.2248	0.0766	0.124	0.011	-0.0125	0.0492	0.0815	0.1086	-19.9742	-0.592	-24.3895
7	2.039	-0.0005	0.5772	0.3997	-0.149	0.2192	0.0872	0.1262	-0.3026	-0.0534	0.038	0.0954	0.0873	-0.0442	-0.103	0.2335	0.1389	-0.0987	1.0155	-0.1131	0.3175	5.7958	-5.5312	-17.5603
8	1.903	0.0747	0.6565	0.9206	0.454	1.4386	-0.0027	-0.2346	0.0201	0.1663	0.032	-0.1107	0.0815	-0.0098	-0.0726	0.3051	0.1596	-0.1109	0.931	-0.0964	0.2806	14.2683	-0.9173	-4.4211
9	3.3937	-0.7457	0.6293	1.6859	-0.0554	0.9234	-0.0403	0.002	0.4539	0.1365	-0.0297	-0.3911	-0.0511	0.1276	0.009	0.168	0.0416	-0.108	0.8088	-0.0817	0.2737	14.7825	5.3297	-10.4698
10	6.2924	1.9516	-0.2002	2.7285	-1.3577	3.6784	-0.0566	0.3103	0.2051	-0.0533	0.1542	0.1259	-0.0654	-0.0358	-0.0945	0.1357	0.0671	-0.0573	0.5742	-0.0196	0.2416	12.9334	3.0141	-13.565
11	3.2265	1.7016	1.7563	3.0046	1.1156	2.8526	0.1121	0.1274	-0.1177	-0.2323	-0.0832	0.0106	0.1132	0.0851	-0.0646	0.1757	-0.0573	0.0062	0.6669	-0.1321	0.2234	10.0415	28.6912	-40.1205
12	2.6901	0.3541	1.3529	3.8392	2.6533	4.1001	-0.1226	-0.0845	0.2856	-0.3939	0.0471	0.2587	-0.4309	0.1386	0.2037	0.189	0.0005	-0.0669	0.6635	0.0706	0.2293	8.4842	45.331	-38.7712
13	1.288	0.0742	0.6328	0.9721	0.2572	0.7969	0.0788	0.0825	-0.1269	-0.1532	0.1063	0.2072	0.0668	-0.0604	-0.025	0.1016	-0.0225	-0.0862	0.7005	0.0754	0.185	2.0698	35.0666	-36.885
14	3.4215	-0.4973	2.7956	1.2322	-1.3612	4.2857	-0.2847	-0.5135	0.3538	0.03	0.0791	0.1806	-0.3348	-0.4197	0.2177	0.1814	0.0696	-0.0878	0.6563	-0.072	0.2344	2.5702	47.2621	-21.7177
15	1.6906	0.696	-0.703	3.5811	-0.2603	1.4409	0.0149	-0.4163	-0.0931	-0.1063	0.0185	0.5486	-0.0391	-0.4849	-0.1155	0.137	0.035	-0.031	0.669	-0.005	0.2424	-0.0702	40.8118	-22.5857
16	0.8172	-0.3396	0.3195	0.5051	0.1563	1.3957	0.0136	-0.09	-0.0405	0.0331	0.0228	-0.0049	0.0194	0.0937	0.0078	0.0642	-0.0192	-0.0007	0.6402	-0.0131	0.0982	12.6341	38.6532	-23.137
17	1.6824	0.2518	0.3115	0.1647	-0.1183	0.3685	0.0996	0.0024	-0.1504	0.0259	-0.0033	-0.0153	0.0823	-0.0254	0.0117	0.2227	0.1031	-0.0523	1.0845	-0.1046	0.2718	38.379	33.3919	-16.4231
18	1.9277	-0.4948	0.3868	1.0324	-0.0135	0.7885	-0.0332	-0.1018	0.1905	0.1402	-0.0049	-0.3009	0.0617	0.2228	-0.0319	0.2009	0.1045	-0.1316	0.8744	-0.0712	0.2799	47.7728	40.5028	-4.7829
19	5.7393	0.5259	1.793	2.5275	-0.1175	1.3823	0.0582	0.2671	0.2164	0.1014	-0.1491	-0.299	-0.0888	0.1652	0.0179	0.2409	-0.0857	-0.0583	0.8961	0.008	0.2052	45.614	43.5836	-10.6802
20	5.7669	1.2399	0.5559	2.565	-0.8521	5.3459	0.0624	0.0922	0.0201	-0.0365	-0.0729	-0.0536	-0.0848	0.1147	0.0745	0.2008	-0.0466	-0.0658	0.5935	0.0738	0.1853	45.1982	40.1281	-10.7786

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resi 98:145
2	X-RAY DIFFRACTION	2	chain A and resi 37:97
3	X-RAY DIFFRACTION	3	chain A and resi 146:233
4	X-RAY DIFFRACTION	4	chain A and resi 234:262
5	X-RAY DIFFRACTION	5	chain A and resi 263:293
6	X-RAY DIFFRACTION	6	chain A and resi 294:405
7	X-RAY DIFFRACTION	7	chain A and resi 406:565
8	X-RAY DIFFRACTION	8	chain A and resi 566:602
9	X-RAY DIFFRACTION	9	chain A and resi 603:661
10	X-RAY DIFFRACTION	10	chain A and resi 662:688
11	X-RAY DIFFRACTION	11	chain B and resi 37:97
12	X-RAY DIFFRACTION	12	chain B and resi 98:145
13	X-RAY DIFFRACTION	13	chain B and resi 146:233
14	X-RAY DIFFRACTION	14	chain B and resi 234:262
15	X-RAY DIFFRACTION	15	chain B and resi 263:293
16	X-RAY DIFFRACTION	16	chain B and resi 294:405
17	X-RAY DIFFRACTION	17	chain B and resi 406:565
18	X-RAY DIFFRACTION	18	chain B and resi 566:629
19	X-RAY DIFFRACTION	19	chain B and resi 630:664
20	X-RAY DIFFRACTION	20	chain B and resi 674:688

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