PDB-9bts: Crystal structure of the bacterioferritin (Bfr) and ferritin (Ftn...

ID or keywords:

Entry

Database: PDB / ID: 9bts

Title

Crystal structure of the bacterioferritin (Bfr) and ferritin (Ftn) heterooligomer complex from Acinetobacter baumannii

Components

Bacterioferritin (Bfr)
Ferritin (Ftn)

Keywords

OXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / heterooligomer / Acinetobacter baumannii

Function / homology

Function and homology information

: / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / heme binding / cytosol
Similarity search - Function

Biological species

Acinetobacter baumannii ATCC 17978 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Lovell, S. / Liu, L. / Battaile, K.P. / Rivera, M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/Office of the Director	S10OD030394	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI169344	United States

Citation

Journal: Sci Rep / Year: 2024
Title: The crystal structure of Acinetobacter baumannii bacterioferritin reveals a heteropolymer of bacterioferritin and ferritin subunits.
Authors: Yao, H. / Alli, S. / Liu, L. / Soldano, A. / Cooper, A. / Fontenot, L. / Verdin, D. / Battaile, K.P. / Lovell, S. / Rivera, M.

History

Deposition	May 15, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2024	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9bts.cif.gz	960.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9bts.ent.gz	804.3 KB	Display	PDB format
PDBx/mmJSON format	9bts.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/bt/9bts ftp://data.pdbj.org/pub/pdb/validation_reports/bt/9bts	HTTPS FTP

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Related structure data

Similar structure data	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	#35 - Nov 2002 Ferritin and Transferrin similarity (6) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Bacterioferritin (Bfr)

B: Bacterioferritin (Bfr)

C: Bacterioferritin (Bfr)

D: Bacterioferritin (Bfr)

E: Bacterioferritin (Bfr)

F: Bacterioferritin (Bfr)

G: Bacterioferritin (Bfr)

H: Bacterioferritin (Bfr)

a: Ferritin (Ftn)

b: Ferritin (Ftn)

c: Ferritin (Ftn)

d: Ferritin (Ftn)

e: Ferritin (Ftn)

f: Ferritin (Ftn)

g: Ferritin (Ftn)

h: Ferritin (Ftn)

hetero molecules

294 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bacterioferritin (Bfr)

B: Bacterioferritin (Bfr)

C: Bacterioferritin (Bfr)

D: Bacterioferritin (Bfr)

E: Bacterioferritin (Bfr)

F: Bacterioferritin (Bfr)

G: Bacterioferritin (Bfr)

H: Bacterioferritin (Bfr)

hetero molecules

A: Bacterioferritin (Bfr)

B: Bacterioferritin (Bfr)

C: Bacterioferritin (Bfr)

D: Bacterioferritin (Bfr)

E: Bacterioferritin (Bfr)

F: Bacterioferritin (Bfr)

G: Bacterioferritin (Bfr)

H: Bacterioferritin (Bfr)

hetero molecules

A: Bacterioferritin (Bfr)

B: Bacterioferritin (Bfr)

C: Bacterioferritin (Bfr)

D: Bacterioferritin (Bfr)

E: Bacterioferritin (Bfr)

F: Bacterioferritin (Bfr)

G: Bacterioferritin (Bfr)

H: Bacterioferritin (Bfr)

hetero molecules

defined by author
Evidence: gel filtration
446 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

a: Ferritin (Ftn)

b: Ferritin (Ftn)

c: Ferritin (Ftn)

d: Ferritin (Ftn)

e: Ferritin (Ftn)

f: Ferritin (Ftn)

g: Ferritin (Ftn)

h: Ferritin (Ftn)

hetero molecules

a: Ferritin (Ftn)

b: Ferritin (Ftn)

c: Ferritin (Ftn)

d: Ferritin (Ftn)

e: Ferritin (Ftn)

f: Ferritin (Ftn)

g: Ferritin (Ftn)

h: Ferritin (Ftn)

hetero molecules

a: Ferritin (Ftn)

b: Ferritin (Ftn)

c: Ferritin (Ftn)

d: Ferritin (Ftn)

e: Ferritin (Ftn)

f: Ferritin (Ftn)

g: Ferritin (Ftn)

h: Ferritin (Ftn)

hetero molecules

defined by author
435 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	173.028, 173.028, 173.028
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	195
Space group name H-M	P23

Components on special symmetry positions

ID	Model	Components
1	1	g-329- HOH

#1: Protein	Bacterioferritin (Bfr) Mass: 18208.629 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria) References: UniProt: A0A1E3M9R5, ferroxidase
#2: Protein	Ferritin (Ftn) Mass: 18058.533 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii ATCC 17978 (bacteria) References: UniProt: T2HRY3, ferroxidase
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 508 / 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: 3 Å³/Da / Density % sol: 66.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Berkeley Screen E5: 1.2 M ammonium sulfate, 100 mM bis-tris pH 6.5, Bfr/Ftn at 12.5 mg/mL. Plate 12825 well E5 drop 1. Puck: PSL-0201, Cryo: 80% (w/v) crystallant and 20% (v/v) glycerol.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 22, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.85→49.95 Å / Num. obs: 146272 / % possible obs: 100 % / Redundancy: 30.4 % / CC_1/2: 1 / R_merge(I) obs: 0.104 / R_pim(I) all: 0.019 / R_rim(I) all: 0.106 / Χ²: 0.98 / Net I/σ(I): 24.6 / Num. measured all: 4450501
Reflection shell	Resolution: 1.85→1.88 Å / % possible obs: 100 % / Redundancy: 31.4 % / R_merge(I) obs: 2.421 / Num. measured all: 227173 / Num. unique obs: 7236 / CC_1/2: 0.716 / R_pim(I) all: 0.439 / R_rim(I) all: 2.461 / Χ²: 0.98 / Net I/σ(I) obs: 1.9

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Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5057	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→24.72 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
Details: The model is a heterocomplex of Bfr and Ftn polypeptides purified from A. baumannii and the both protein overlap at the same sites throughout the polypeptide. Group occupancy refinement was ...

	R_factor	Num. reflection	% reflection
R_free	0.1989	7527	5.15 %
R_work	0.166	-	-
obs	0.1677	146118	99.94 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→24.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19938	0	222	508	20668

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	20506
X-RAY DIFFRACTION	f_angle_d	0.891	27790
X-RAY DIFFRACTION	f_dihedral_angle_d	14.546	7594
X-RAY DIFFRACTION	f_chiral_restr	0.047	3040
X-RAY DIFFRACTION	f_plane_restr	0.008	3592

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 (%)
1.85-1.87	0.2771	222	0.2182	4599	X-RAY DIFFRACTION	100
1.87-1.89	0.2744	229	0.214	4677	X-RAY DIFFRACTION	100
1.89-1.92	0.2629	241	0.1977	4536	X-RAY DIFFRACTION	100
1.92-1.94	0.2522	232	0.1953	4606	X-RAY DIFFRACTION	100
1.94-1.97	0.2343	280	0.1835	4566	X-RAY DIFFRACTION	100
1.97-1.99	0.2346	222	0.1811	4646	X-RAY DIFFRACTION	100
1.99-2.02	0.2479	227	0.1735	4597	X-RAY DIFFRACTION	100
2.02-2.05	0.1991	245	0.1674	4595	X-RAY DIFFRACTION	100
2.05-2.08	0.2309	248	0.1626	4588	X-RAY DIFFRACTION	100
2.08-2.12	0.2146	261	0.1571	4570	X-RAY DIFFRACTION	100
2.12-2.15	0.2121	280	0.1513	4570	X-RAY DIFFRACTION	100
2.15-2.19	0.1911	265	0.1496	4589	X-RAY DIFFRACTION	100
2.19-2.24	0.1815	256	0.1483	4582	X-RAY DIFFRACTION	100
2.24-2.28	0.1969	242	0.1483	4597	X-RAY DIFFRACTION	100
2.28-2.33	0.2096	212	0.1498	4681	X-RAY DIFFRACTION	100
2.33-2.38	0.1815	250	0.1564	4579	X-RAY DIFFRACTION	100
2.38-2.44	0.1768	242	0.1523	4626	X-RAY DIFFRACTION	100
2.44-2.51	0.1859	290	0.1515	4558	X-RAY DIFFRACTION	100
2.51-2.58	0.1958	269	0.1598	4619	X-RAY DIFFRACTION	100
2.58-2.67	0.1993	243	0.1622	4612	X-RAY DIFFRACTION	100
2.67-2.76	0.1898	251	0.1645	4626	X-RAY DIFFRACTION	100
2.76-2.87	0.1885	240	0.1609	4597	X-RAY DIFFRACTION	100
2.87-3	0.2021	241	0.1684	4641	X-RAY DIFFRACTION	100
3-3.16	0.2115	266	0.18	4625	X-RAY DIFFRACTION	100
3.16-3.36	0.1897	257	0.1683	4645	X-RAY DIFFRACTION	100
3.36-3.62	0.1975	257	0.1573	4639	X-RAY DIFFRACTION	100
3.62-3.98	0.1633	209	0.1557	4688	X-RAY DIFFRACTION	100
3.98-4.55	0.1729	279	0.1408	4696	X-RAY DIFFRACTION	100
4.55-5.72	0.1783	282	0.172	4669	X-RAY DIFFRACTION	100
5.73-24.72	0.2544	289	0.2096	4772	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	1.0264	-0.7443	0.4799	0.5715	-0.3789	0.5948	0.07	0.0612	0.0021	-0.1007	-0.0746	-0.0063	0.1381	0.0077	-0.0213	0.222	-0.0357	0.0068	0.1987	-0.0373	0.2231	16.4964	3.8064	33.0205
2	0.6725	-0.3176	0.3613	0.4445	-0.379	0.5836	-0.0082	-0.1565	-0.0036	0.0287	0.0437	0.054	-0.0579	-0.0757	-0.0108	0.2494	-0.0237	0.0284	0.2111	-0.024	0.2352	33.9385	69.2759	83.395
3	1.0854	-0.453	0.4361	0.7754	-0.7073	0.783	-0.0313	0.0504	0.1995	-0.0077	-0.005	-0.1182	-0.0261	0.0166	0.0205	0.2247	-0.0154	0.0033	0.2199	-0.0293	0.2175	52.8796	81.2549	72.3573
4	0.9606	0.5311	0.7983	0.6609	0.53	0.6795	-0.0707	-0.1533	0.1005	-0.0247	-0.05	0.0829	-0.0699	-0.094	0.1097	0.2588	-0.0212	0.0524	0.2467	-0.0093	0.1679	17.7	30.5196	82.4319
5	0.4879	0.2527	0.4555	0.5945	0.3732	0.7008	0.056	-0.0947	-0.0355	0.1477	0.0284	0.0663	0.0607	-0.1119	-0.0837	0.2261	-0.0106	0.0562	0.2383	-0.0208	0.2203	5.6521	50.6586	72.8838
6	0.7277	-0.4623	-0.3643	0.6656	0.5735	0.7759	-0.0428	0.0676	-0.0751	0.0693	-0.0326	0.0038	0.1009	0.0219	0.0453	0.2415	0.0175	0.0155	0.212	0.0359	0.2084	55.8924	14.545	80.2712
7	0.5382	-0.3534	-0.2015	0.4394	0.469	0.5766	0.0545	-0.0106	-0.0046	-0.0165	-0.032	0.0379	-0.0527	0.0114	-0.0233	0.2175	-0.0201	0.023	0.1888	0.04	0.2733	35.724	3.4501	69.7575
8	0.6875	-0.4964	0.3701	0.7153	-0.2205	0.4474	0.0946	0.0956	-0.0487	0.0186	-0.1021	0.0571	0.1267	0.0238	0.0232	0.2026	-0.0684	-0.0028	0.2058	0.0296	0.2069	6.3365	13.6553	53.6608
9	0.7491	-0.4714	0.1715	0.6276	-0.3602	0.4034	-0.0613	-0.0299	-0.0295	-0.0112	0.079	0.0021	-0.023	-0.0478	-0.0101	0.2479	-0.0548	-0.0303	0.2061	-0.0184	0.2142	16.8648	4.1648	32.628
10	0.4521	-0.3973	0.3764	0.6343	-0.2955	0.3684	-0.0051	-0.0341	0.0267	0.0319	-0.0573	0.0135	0.0097	-0.052	0.0502	0.2313	0.024	-0.0052	0.2278	-0.0456	0.2177	33.5705	68.9774	83.1674
11	0.5239	-0.5109	0.4081	0.5242	-0.4616	0.6211	-0.0279	-0.0802	0.0123	0.0166	0.0485	0.0599	-0.0124	-0.0174	-0.0148	0.2435	-0.0051	-0.0209	0.1923	-0.0674	0.2086	52.9122	81.0778	72.0425
12	0.7808	0.1766	0.6529	0.662	0.313	0.7375	0.0204	-0.0446	-0.1395	0.1292	0.0264	-0.0217	0.123	-0.0255	-0.028	0.2237	0.0068	0.0187	0.2528	0.0241	0.2486	17.1539	30.8664	82.7684
13	0.83	0.1939	0.7031	0.5643	0.5087	1.063	-0.0301	0.0506	0.1101	-0.0672	-0.0649	0.1056	-0.0505	0.0182	0.0641	0.2222	0.0013	0.0307	0.2353	0.0195	0.2393	5.2653	50.6141	72.8718
14	0.6457	-0.0392	-0.297	0.803	0.6505	0.8608	0.0068	-0.1523	0.0113	0.0933	0.0283	-0.0208	0.0819	0.0933	-0.0105	0.2722	-0.0253	-0.0338	0.2639	0.0262	0.2244	55.8556	14.1807	80.4398
15	0.4953	-0.3459	-0.4625	0.5962	0.357	0.4696	-0.012	0.0491	-0.0892	0.0056	0.0049	0.0601	0.0458	-0.0761	-0.0215	0.2664	-0.0374	-0.0238	0.2607	0.0179	0.2157	35.9684	3.1268	69.9338
16	0.7653	-0.6119	0.2728	0.8267	-0.4301	0.6376	-0.0353	-0.1195	-0.0152	0.0223	0.096	0.0246	-0.0257	-0.1651	-0.0483	0.2087	-0.0296	0.0005	0.2381	-0.0322	0.2194	6.0602	13.4241	53.6674

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'F' and resid 1 through 154)
2	X-RAY DIFFRACTION	2	(chain 'G' and resid 1 through 154)
3	X-RAY DIFFRACTION	3	(chain 'H' and resid 1 through 154)
4	X-RAY DIFFRACTION	4	(chain 'a' and resid 1 through 154)
5	X-RAY DIFFRACTION	5	(chain 'b' and resid 1 through 154)
6	X-RAY DIFFRACTION	6	(chain 'c' and resid 1 through 154)
7	X-RAY DIFFRACTION	7	(chain 'd' and resid 1 through 154)
8	X-RAY DIFFRACTION	8	(chain 'e' and resid 1 through 154)
9	X-RAY DIFFRACTION	9	(chain 'f' and resid 1 through 154)
10	X-RAY DIFFRACTION	10	(chain 'g' and resid 1 through 154)
11	X-RAY DIFFRACTION	11	(chain 'h' and resid 1 through 154)
12	X-RAY DIFFRACTION	12	(chain 'A' and resid 1 through 154)
13	X-RAY DIFFRACTION	13	(chain 'B' and resid 1 through 154)
14	X-RAY DIFFRACTION	14	(chain 'C' and resid 1 through 154)
15	X-RAY DIFFRACTION	15	(chain 'D' and resid 1 through 154)
16	X-RAY DIFFRACTION	16	(chain 'E' and resid 1 through 154)

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