PDB-3bkn: The structure of Mycobacterial bacterioferritin

ID or keywords:

Entry

Database: PDB / ID: 3bkn

Title

The structure of Mycobacterial bacterioferritin

Components

Bacterioferritin

Keywords

METAL BINDING PROTEIN / BACTERIOFERRITIN / CYTOCHROM B1 / MYCOBACTERIUM SMEGMATIS / HEME / IRON / IRON STORAGE / METAL-BINDING

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

Mycobacterium smegmatis str. MC2 155 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.72 Å

Authors

Janowski, R. / Auerbach-Nevo, T. / Weiss, M.S.

Citation

Journal: Protein Sci. / Year: 2008
Title: Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site.
Authors: Janowski, R. / Auerbach-Nevo, T. / Weiss, M.S.

History

Deposition	Dec 7, 2007	Deposition site: RCSB / Processing site: PDBJ
Supersession	Jan 22, 2008	ID: 3B3H
Revision 1.0	Jan 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bkn.cif.gz	396.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3bkn.ent.gz	330 KB	Display	PDB format
PDBx/mmJSON format	3bkn.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/bk/3bkn ftp://data.pdbj.org/pub/pdb/validation_reports/bk/3bkn	HTTPS FTP

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Related structure data

Related structure data	1sofS S: Starting model for refinement
Similar structure data	3uof-1 3uoi-2 3e1m-1 3gvy-1 3uoi-1 1jgc-1 5d8s-1 6nlf-1 3ghq-1 3e1p-1 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	#35 - Nov 2002 Ferritin and Transferrin similarity (6) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

E: Bacterioferritin

F: Bacterioferritin

G: Bacterioferritin

H: Bacterioferritin

I: Bacterioferritin

J: Bacterioferritin

K: Bacterioferritin

L: Bacterioferritin

hetero molecules

229 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

E: Bacterioferritin

F: Bacterioferritin

G: Bacterioferritin

H: Bacterioferritin

I: Bacterioferritin

J: Bacterioferritin

K: Bacterioferritin

L: Bacterioferritin

hetero molecules

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

E: Bacterioferritin

F: Bacterioferritin

G: Bacterioferritin

H: Bacterioferritin

I: Bacterioferritin

J: Bacterioferritin

K: Bacterioferritin

L: Bacterioferritin

hetero molecules

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

Unit cell

Length a, b, c (Å)	181.523, 151.520, 116.715
Angle α, β, γ (deg.)	90.00, 128.08, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	K-301- HEM
2	1	K-301- HEM
3	1	K-301- HEM
4	1	L-301- HEM
5	1	L-301- HEM
6	1	L-301- HEM

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 1 - 155 / Label seq-ID: 1 - 155

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J
11	K	K
12	L	L

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein	Bacterioferritin Mass: 18500.834 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: mc(2)155 / References: UniProt: A0QY79

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Non-polymers , 5 types, 86 molecules

#2: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.77 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 10% (v/v) 2-propanol, 14% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.905 Å
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 2007 / Details: Si(111) monochromator
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.905 Å / Relative weight: 1
Reflection	Resolution: 2.72→30 Å / Num. all: 65786 / Num. obs: 65786 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / B_iso Wilson estimate: 43.7 Å² / R_merge(I) obs: 0.11 / R_sym value: 0.11 / Net I/σ(I): 10
Reflection shell	Resolution: 2.72→2.76 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3302 / R_sym value: 0.528 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MAR345dtb		data collection
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1sof

1sof

Resolution: 2.72→29.64 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.885 / SU B: 21.95 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS and NCS used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22828	2649	4 %	RANDOM
R_work	0.17947	-	-	-
all	0.18144	63129	-	-
obs	0.18144	63129	98.78 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 46.756 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.35 Å²	0 Å²	-0.71 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	-0.99 Å²

Refinement step

Cycle: LAST / Resolution: 2.72→29.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15564	0	367	41	15972

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	16455
X-RAY DIFFRACTION	r_angle_refined_deg	1.715	2.079	22429
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.646	5	1926
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.277	25.018	843
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.814	15	2910
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.701	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.115	0.2	2427
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	12540
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	7670
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	11152
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	473
X-RAY DIFFRACTION	r_metal_ion_refined	0.121	0.2	48
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.226	0.2	164
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.21	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.028	2	9913
X-RAY DIFFRACTION	r_mcangle_it	1.695	3	15474
X-RAY DIFFRACTION	r_scbond_it	1.752	2	7337
X-RAY DIFFRACTION	r_scangle_it	3.03	10	6928

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	618	tight positional	0.05	0.05
2	B	618	tight positional	0.05	0.05
3	C	618	tight positional	0.05	0.05
4	D	618	tight positional	0.06	0.05
5	E	618	tight positional	0.05	0.05
6	F	618	tight positional	0.05	0.05
7	G	618	tight positional	0.06	0.05
8	H	618	tight positional	0.05	0.05
9	I	618	tight positional	0.05	0.05
10	J	618	tight positional	0.06	0.05
11	K	618	tight positional	0.05	0.05
12	L	618	tight positional	0.05	0.05
1	A	627	medium positional	0.49	0.5
2	B	627	medium positional	0.47	0.5
3	C	627	medium positional	0.34	0.5
4	D	627	medium positional	0.5	0.5
5	E	627	medium positional	0.37	0.5
6	F	627	medium positional	0.37	0.5
7	G	627	medium positional	0.32	0.5
8	H	627	medium positional	0.32	0.5
9	I	627	medium positional	0.35	0.5
10	J	627	medium positional	0.39	0.5
11	K	627	medium positional	0.39	0.5
12	L	627	medium positional	0.33	0.5
1	A	618	tight thermal	0.13	0.5
2	B	618	tight thermal	0.13	0.5
3	C	618	tight thermal	0.13	0.5
4	D	618	tight thermal	0.12	0.5
5	E	618	tight thermal	0.12	0.5
6	F	618	tight thermal	0.12	0.5
7	G	618	tight thermal	0.13	0.5
8	H	618	tight thermal	0.13	0.5
9	I	618	tight thermal	0.12	0.5
10	J	618	tight thermal	0.12	0.5
11	K	618	tight thermal	0.11	0.5
12	L	618	tight thermal	0.11	0.5
1	A	627	medium thermal	0.92	2
2	B	627	medium thermal	1.03	2
3	C	627	medium thermal	0.96	2
4	D	627	medium thermal	1.03	2
5	E	627	medium thermal	0.91	2
6	F	627	medium thermal	0.83	2
7	G	627	medium thermal	0.98	2
8	H	627	medium thermal	0.92	2
9	I	627	medium thermal	0.88	2
10	J	627	medium thermal	1.08	2
11	K	627	medium thermal	0.93	2
12	L	627	medium thermal	0.92	2

LS refinement shell

Resolution: 2.72→2.866 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.273	349	-
R_work	0.243	8839	-
obs	-	-	95.39 %

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	0.8415	-0.9261	-0.0801	2.0556	0.1526	0.6793	0.0172	0.0206	-0.0667	-0.1763	0.1062	0.0031	-0.1203	0.0122	-0.1235	-0.1161	-0.0029	-0.0243	-0.161	0.0388	-0.0896	11.5383	2.4771	-39.2363
2	0.9129	-0.3857	-0.6242	1.1577	1.009	1.7444	0.0689	0.1075	0.0359	-0.1627	-0.0069	0.0692	-0.1825	-0.1617	-0.062	-0.0894	0.0359	-0.0124	-0.0543	0.059	-0.1423	-12.9702	-2.8147	-41.905
3	1.0028	0.1098	0.7003	0.6752	0.3878	2.5758	-0.0292	-0.0481	0.1058	-0.067	-0.0466	-0.0296	-0.0721	0.3047	0.0758	-0.1948	-0.0344	-0.016	-0.0581	0.0029	-0.0247	43.3668	-10.9179	-17.4794
4	0.5093	-0.0295	-0.2561	0.6996	0.0753	2.6899	-0.0088	-0.0498	0.0682	0.0271	0.0363	-0.0029	-0.1161	0.2144	-0.0276	-0.1183	-0.0955	0.004	-0.1049	-0.0234	-0.0416	32.4859	10.6049	-10.8567
5	0.6376	-0.0238	-0.0389	1.2079	0.5214	1.1138	-0.0475	-0.18	-0.0393	-0.0119	0.0331	-0.1934	0.0672	0.3053	0.0144	-0.1203	0.0641	-0.0328	0.0773	0.0291	-0.0924	33.4405	-31.8699	34.1989
6	1.1233	-0.7008	-0.0485	1.8208	0.1532	0.4749	-0.0149	-0.167	0.0125	0.1306	0.0049	-0.0245	-0.0496	0.3359	0.01	-0.1564	-0.0045	-0.0297	0.1127	0.0051	-0.0711	44.0377	-15.3249	18.648
7	2.2617	0.5603	0.1463	0.4191	0.221	0.7124	0.0181	0.2631	-0.0354	-0.0707	-0.04	-0.0644	0.1101	-0.0833	0.0218	-0.0868	-0.0394	-0.0132	-0.1254	-0.0218	-0.1151	0.3913	-36.1232	-46.8555
8	1.6673	0.2008	-0.4322	0.3406	-0.1513	0.9535	-0.003	0.0703	-0.0407	0.0109	-0.0235	-0.0042	0.232	-0.082	0.0265	0.0267	-0.0641	0.0535	-0.1309	-0.0692	-0.1148	-1.7817	-57.7398	-34.2745
9	0.736	0.2792	-0.2651	2.107	-0.9403	1.1625	-0.1447	0.0281	-0.0696	-0.0065	0.0614	-0.1493	0.1505	0.0735	0.0832	-0.066	0.0832	0.0167	-0.1229	0.0067	-0.0882	32.2575	-49.5629	-25.0651
10	0.6203	0.2265	-0.3602	1.2784	-0.5793	1.6135	-0.1021	-0.0533	-0.0438	-0.003	0.048	-0.1064	0.1754	0.1449	0.0541	-0.1432	0.1461	0.0116	0.0009	0.0482	-0.0623	43.5695	-44.3006	-3.3187
11	2.5871	0.5745	0.1871	0.6564	0.1138	0.7623	0.1441	0.0299	0.1898	0.0203	-0.0452	0.0289	-0.2844	-0.0806	-0.0989	0.0018	0.0131	0.0392	-0.1582	0.0194	-0.0648	-1.5124	23.3908	-12.4667
12	0.7581	0.2532	0.8383	0.8137	0.5927	2.1672	-0.1191	-0.0657	-0.146	0.0636	-0.0681	-0.0126	0.4661	0.0153	0.1871	0.0898	0.0485	0.1152	-0.1384	0.0032	-0.0482	12.1043	-70.538	-3.2689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 161	1 - 161
2	X-RAY DIFFRACTION	2	B	B	1 - 161	1 - 161
3	X-RAY DIFFRACTION	3	C	C	1 - 161	1 - 161
4	X-RAY DIFFRACTION	4	D	D	1 - 161	1 - 161
5	X-RAY DIFFRACTION	5	E	E	1 - 161	1 - 161
6	X-RAY DIFFRACTION	6	F	F	1 - 161	1 - 161
7	X-RAY DIFFRACTION	7	G	G	1 - 161	1 - 161
8	X-RAY DIFFRACTION	8	H	H	1 - 161	1 - 161
9	X-RAY DIFFRACTION	9	I	I	1 - 161	1 - 161
10	X-RAY DIFFRACTION	10	J	J	1 - 161	1 - 161
11	X-RAY DIFFRACTION	11	K	K	1 - 161	1 - 161
12	X-RAY DIFFRACTION	12	L	L	1 - 161	1 - 161

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

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Non-polymers , 5 types, 86 molecules

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