PDB-2htn: E. coli bacterioferritin in its as-isolated form

ID or keywords:

Entry

Database: PDB / ID: 2htn

Title

E. coli bacterioferritin in its as-isolated form

Components

Bacterioferritin

Keywords

METAL BINDING PROTEIN / OXIDOREDUCTASE / four-helix bundle / ferroxidase centre / haem / protein shell / iron binding site

Function / homology

Function and homology information

iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

van Eerde, A. / Wolterink-Van Loo, S. / Van Der Oost, J. / Dijkstra, B.W.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.
Authors: van Eerde, A. / Wolterink-van Loo, S. / van der Oost, J. / Dijkstra, B.W.

History

Deposition	Jul 26, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3	Nov 12, 2014	Group: Derived calculations
Revision 1.4	Aug 30, 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_conn_angle / 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 / _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_alt_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_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_alt_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Aug 12, 2026	Group: Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_struct_conn_angle / struct_conn Item: _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id ..._pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id Description: Metalloprotein remediation / Provider: repository / Type: Remediation

Remark 600

HETEROGEN Authors state that the oxidation state of Fe could be an Fe(II) or FE(III) ion. Authors ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2htn.cif.gz	273.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2htn.ent.gz	225.3 KB	Display	PDB format
PDBx/mmJSON format	2htn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/2htn ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2htn	HTTPS FTP

-
Related structure data

Related structure data	1bcfS S: Starting model for refinement
Similar structure data	6p8l-1 4tod-d 3isf-1 2vxi-1 3ise-d 2y3q-1 4u3g-1 6p8k-1 5d8r-1 1nf4-2 3ghq-1 5d8o-1 4toh-1 3e1q-1 5d8p-1 1nf4-3 1bcf-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

-
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

hetero molecules

152 kDa, 8 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

hetero molecules

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

E: Bacterioferritin

F: Bacterioferritin

G: Bacterioferritin

H: Bacterioferritin

hetero molecules

A: Bacterioferritin

B: Bacterioferritin

C: Bacterioferritin

D: Bacterioferritin

E: Bacterioferritin

F: Bacterioferritin

G: Bacterioferritin

H: Bacterioferritin

hetero molecules

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

Unit cell

Length a, b, c (Å)	167.893, 167.893, 167.893
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	ASN	ASN	A	A	1 - 17	1 - 17
2	1	1	MET	MET	ASN	ASN	B	B	1 - 17	1 - 17
3	1	1	MET	MET	ASN	ASN	C	C	1 - 17	1 - 17
4	1	1	MET	MET	ASN	ASN	D	D	1 - 17	1 - 17
5	1	1	MET	MET	ASN	ASN	E	E	1 - 17	1 - 17
6	1	1	MET	MET	ASN	ASN	F	F	1 - 17	1 - 17
7	1	1	MET	MET	ASN	ASN	G	G	1 - 17	1 - 17
8	1	1	MET	MET	ASN	ASN	H	H	1 - 17	1 - 17
9	2	1	LEU	LEU	ASP	ASP	A	A	19 - 50	19 - 50
10	2	1	LEU	LEU	ASP	ASP	B	B	19 - 50	19 - 50
11	2	1	LEU	LEU	ASP	ASP	C	C	19 - 50	19 - 50
12	2	1	LEU	LEU	ASP	ASP	D	D	19 - 50	19 - 50
13	2	1	LEU	LEU	ASP	ASP	E	E	19 - 50	19 - 50
14	2	1	LEU	LEU	ASP	ASP	F	F	19 - 50	19 - 50
15	2	1	LEU	LEU	ASP	ASP	G	G	19 - 50	19 - 50
16	2	1	LEU	LEU	ASP	ASP	H	H	19 - 50	19 - 50
17	3	1	MET	MET	LYS	LYS	A	A	52 - 53	52 - 53
18	3	1	MET	MET	LYS	LYS	B	B	52 - 53	52 - 53
19	3	1	MET	MET	LYS	LYS	C	C	52 - 53	52 - 53
20	3	1	MET	MET	LYS	LYS	D	D	52 - 53	52 - 53
21	3	1	MET	MET	LYS	LYS	E	E	52 - 53	52 - 53
22	3	1	MET	MET	LYS	LYS	F	F	52 - 53	52 - 53
23	3	1	MET	MET	LYS	LYS	G	G	52 - 53	52 - 53
24	3	1	MET	MET	LYS	LYS	H	H	52 - 53	52 - 53
25	4	1	ALA	ALA	LEU	LEU	A	A	55 - 93	55 - 93
26	4	1	ALA	ALA	LEU	LEU	B	B	55 - 93	55 - 93
27	4	1	ALA	ALA	LEU	LEU	C	C	55 - 93	55 - 93
28	4	1	ALA	ALA	LEU	LEU	D	D	55 - 93	55 - 93
29	4	1	ALA	ALA	LEU	LEU	E	E	55 - 93	55 - 93
30	4	1	ALA	ALA	LEU	LEU	F	F	55 - 93	55 - 93
31	4	1	ALA	ALA	LEU	LEU	G	G	55 - 93	55 - 93
32	4	1	ALA	ALA	LEU	LEU	H	H	55 - 93	55 - 93
33	5	1	LEU	LEU	ASP	ASP	A	A	95 - 126	95 - 126
34	5	1	LEU	LEU	ASP	ASP	B	B	95 - 126	95 - 126
35	5	1	LEU	LEU	ASP	ASP	C	C	95 - 126	95 - 126
36	5	1	LEU	LEU	ASP	ASP	D	D	95 - 126	95 - 126
37	5	1	LEU	LEU	ASP	ASP	E	E	95 - 126	95 - 126
38	5	1	LEU	LEU	ASP	ASP	F	F	95 - 126	95 - 126
39	5	1	LEU	LEU	ASP	ASP	G	G	95 - 126	95 - 126
40	5	1	LEU	LEU	ASP	ASP	H	H	95 - 126	95 - 126
41	6	1	GLU	GLU	GLY	GLY	A	A	128 - 129	128 - 129
42	6	1	GLU	GLU	GLY	GLY	B	B	128 - 129	128 - 129
43	6	1	GLU	GLU	GLY	GLY	C	C	128 - 129	128 - 129
44	6	1	GLU	GLU	GLY	GLY	D	D	128 - 129	128 - 129
45	6	1	GLU	GLU	GLY	GLY	E	E	128 - 129	128 - 129
46	6	1	GLU	GLU	GLY	GLY	F	F	128 - 129	128 - 129
47	6	1	GLU	GLU	GLY	GLY	G	G	128 - 129	128 - 129
48	6	1	GLU	GLU	GLY	GLY	H	H	128 - 129	128 - 129
1	1	2	MET	MET	HEM	HEM	A	A - K	1 - 200	1
2	1	2	MET	MET	HEM	HEM	C	C - P	1 - 200	1
3	1	2	MET	MET	HEM	HEM	E	E - U	1 - 200	1
4	1	2	MET	MET	HEM	HEM	G	G - Z	1 - 200	1

NCS ensembles :

ID
1
2

Details

The biological assembly is a 24-mer generated from the octamer in the asymmetric unit by the operations: y+1/2,-z+1/2,-x and -z,x+1/2,-y+1/2.

#1: Protein	Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557 Mass: 18518.016 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: UniProt: P0ABD3, ferroxidase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.79 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% (v/v) PEG400, 0.2M MGCl2, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 11, 2004
Radiation	Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.3→74.54 Å / Num. all: 69975 / Num. obs: 69835 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.3→2.42 Å / % possible all: 98.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BCF

1bcf

Resolution: 2.5→59.34 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.918 / SU B: 6.806 / SU ML: 0.155 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 1.045 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2) FINAL REFINEMENT WAS DONE USING DETWINNED DATA 3) the crystallographic data used for solving this structure was perfectly twinned.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18803	5633	10.3 %	IN THIN SHELLS
R_work	0.17059	-	-	-
all	0.17243	54648	-	-
obs	0.17243	54540	99.8 %	-

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: 22.727 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→59.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10392	0	188	98	10678

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	10944
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	7320
X-RAY DIFFRACTION	r_angle_refined_deg	1.162	2.072	14832
X-RAY DIFFRACTION	r_angle_other_deg	2.027	3	17800
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.024	5	1256
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	46.235	25.27	592
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.021	15	2056
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.549	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1528
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	12096
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2040
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	3291
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	7739
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.5	5546
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.5	5323
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.4	457
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.01	0.4	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.133	10	8
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.38	0.2	69
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.432	0.2	160
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.325	0.4	28
X-RAY DIFFRACTION	r_mcbond_it	6.734	1.5	8409
X-RAY DIFFRACTION	r_mcbond_other	1.59	1.5	2600
X-RAY DIFFRACTION	r_mcangle_it	6.946	2	9960
X-RAY DIFFRACTION	r_scbond_it	11.931	3	5555
X-RAY DIFFRACTION	r_scangle_it	13.009	4.5	4856

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1711	tight positional	0	0
1	2	B	1711	tight positional	0	0
1	3	C	1711	tight positional	0	0
1	4	D	1711	tight positional	0	0
1	5	E	1711	tight positional	0	0
1	6	F	1711	tight positional	0	0
1	7	G	1711	tight positional	0	0
1	8	H	1711	tight positional	0	0
2	1	A	2196	tight positional	0	0
2	2	C	2196	tight positional	0	0
2	3	E	2196	tight positional	0	0
2	2	F	2196	tight positional	0	0
1	1	A	1711	tight thermal	0.38	0.1
1	2	B	1711	tight thermal	0.59	0.1
1	3	C	1711	tight thermal	0.41	0.1
1	4	D	1711	tight thermal	0.58	0.1
1	5	E	1711	tight thermal	0.37	0.1
1	6	F	1711	tight thermal	0.4	0.1
1	7	G	1711	tight thermal	0.58	0.1
1	8	H	1711	tight thermal	0.57	0.1
2	1	A	2196	tight thermal	0.4	0.1
2	2	C	2196	tight thermal	0.41	0.1
2	3	E	2196	tight thermal	0.42	0.1
2	2	F	2196	tight thermal	0.47	0.1

LS refinement shell

Resolution: 2.5→2.572 Å / Total num. of bins used: 18 /

	R_factor	Num. reflection
R_free	0.179	-
R_work	0.199	4013

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi