PDB-3uno: Mycobacterium tuberculosis ferritin homolog, BfrB

ID or keywords:

Entry

Database: PDB / ID: 3uno

Title

Mycobacterium tuberculosis ferritin homolog, BfrB

Components

Probable bacterioferritin BfrB

Keywords

OXIDOREDUCTASE / ferritin / ferroxidase activity / iron storage / Structural Genomics / TB Structural Genomics Consortium / TBSGC

Function / homology

Function and homology information

Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / peptidoglycan-based cell wall / ferrous iron binding / iron ion transport ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.503 Å

Authors

McMath, L.M. / Contreras, H. / Goulding, C.W. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: Mycobacterium tuberculosis ferritin homolog, BfrB
Authors: McMath, L.M. / Contreras, H. / Goulding, C.W.

History

Deposition	Nov 16, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3uno.cif.gz	820.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3uno.ent.gz	687.1 KB	Display	PDB format
PDBx/mmJSON format	3uno.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3oj5C C: citing same article (ref.)
Similar structure data	3kx9-d 2fkz-1 30103 3fvb-1 2jd6-2 4iwk-1 3r2h-1 3r2s-1 9890 6a4u-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: TB-Rv3841

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (8) #193 - Jan 2016 Siderocalin similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Probable bacterioferritin BfrB

B: Probable bacterioferritin BfrB

C: Probable bacterioferritin BfrB

D: Probable bacterioferritin BfrB

E: Probable bacterioferritin BfrB

F: Probable bacterioferritin BfrB

G: Probable bacterioferritin BfrB

H: Probable bacterioferritin BfrB

I: Probable bacterioferritin BfrB

J: Probable bacterioferritin BfrB

K: Probable bacterioferritin BfrB

L: Probable bacterioferritin BfrB

M: Probable bacterioferritin BfrB

N: Probable bacterioferritin BfrB

O: Probable bacterioferritin BfrB

P: Probable bacterioferritin BfrB

Q: Probable bacterioferritin BfrB

R: Probable bacterioferritin BfrB

S: Probable bacterioferritin BfrB

T: Probable bacterioferritin BfrB

U: Probable bacterioferritin BfrB

V: Probable bacterioferritin BfrB

W: Probable bacterioferritin BfrB

X: Probable bacterioferritin BfrB

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	226.234, 226.750, 113.678
Angle α, β, γ (deg.)	90.00, 94.75, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	O-229- HOH
2	1	O-237- HOH
3	1	S-211- HOH
4	1	S-266- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

#1: Protein	... Probable bacterioferritin BfrB / Non-heme ferritin Ftn / Nox19 Mass: 21436.947 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bfrB, ftn, MT3949 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96237, UniProt: P9WNE5*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2143 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

...
Probable bacterioferritin BfrB / Non-heme ferritin Ftn / Nox19

Mass: 21436.947 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Gene: bfrB, ftn, MT3949 / Plasmid: pET28b+ / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96237, UniProt: P9WNE5*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 2143 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.44 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 11.9%(w/v) PEG MME 5000, 100 mM Tris maleate, 0.54%(w/v) 1,6-hexanediol, 0.44%(w/v) lauryldimethylamine oxide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2005
Radiation	Monochromator: liquid nitrogen cooled dual crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 19297 / % possible obs: 99.9 %

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.503→49.352 Å / SU ML: 0.75 / σ(F): 0 / Phase error: 27.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2471	19306	9.95 %	10%
R_work	0.2058	-	-	-
obs	0.21	19297	99.13 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 38.679 Å² / k_sol: 0.356 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.4309 Å²	0 Å²	1.3371 Å²
2-	-	-0.6259 Å²	0 Å²
3-	-	-	3.0568 Å²

Refinement step

Cycle: LAST / Resolution: 2.503→49.352 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	32424	0	0	2143	34567

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	32948
X-RAY DIFFRACTION	f_angle_d	1.249	44529
X-RAY DIFFRACTION	f_dihedral_angle_d	16.861	12125
X-RAY DIFFRACTION	f_chiral_restr	0.086	4905
X-RAY DIFFRACTION	f_plane_restr	0.006	6007

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1340	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1340	X-RAY DIFFRACTION	POSITIONAL	0.105
1	3	C	1340	X-RAY DIFFRACTION	POSITIONAL	0.12
1	4	D	1340	X-RAY DIFFRACTION	POSITIONAL	0.108
1	5	E	1340	X-RAY DIFFRACTION	POSITIONAL	0.087
1	6	F	1340	X-RAY DIFFRACTION	POSITIONAL	0.111
1	7	G	1333	X-RAY DIFFRACTION	POSITIONAL	0.117
1	8	H	1336	X-RAY DIFFRACTION	POSITIONAL	0.078
1	9	I	1340	X-RAY DIFFRACTION	POSITIONAL	0.122
1	10	J	1340	X-RAY DIFFRACTION	POSITIONAL	0.135
1	11	K	1340	X-RAY DIFFRACTION	POSITIONAL	0.082
1	12	L	1340	X-RAY DIFFRACTION	POSITIONAL	0.116
1	13	M	1340	X-RAY DIFFRACTION	POSITIONAL	0.113
1	14	N	1340	X-RAY DIFFRACTION	POSITIONAL	0.082
1	15	O	1338	X-RAY DIFFRACTION	POSITIONAL	0.127
1	16	P	1340	X-RAY DIFFRACTION	POSITIONAL	0.118
1	17	Q	1329	X-RAY DIFFRACTION	POSITIONAL	0.115
1	18	R	1340	X-RAY DIFFRACTION	POSITIONAL	0.105
1	19	S	1332	X-RAY DIFFRACTION	POSITIONAL	0.079
1	20	T	1340	X-RAY DIFFRACTION	POSITIONAL	0.101
1	21	U	1340	X-RAY DIFFRACTION	POSITIONAL	0.122
1	22	V	1340	X-RAY DIFFRACTION	POSITIONAL	0.12
1	23	W	1340	X-RAY DIFFRACTION	POSITIONAL	0.112
1	24	X	1340	X-RAY DIFFRACTION	POSITIONAL	0.07

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 (%)
2.503-2.5315	0.3028	468	0.2449	4837	X-RAY DIFFRACTION	82
2.5315-2.5613	0.3149	669	0.2431	5840	X-RAY DIFFRACTION	100
2.5613-2.5925	0.2919	666	0.2303	5862	X-RAY DIFFRACTION	100
2.5925-2.6253	0.2665	615	0.2207	5885	X-RAY DIFFRACTION	100
2.6253-2.6599	0.276	608	0.1977	5863	X-RAY DIFFRACTION	100
2.6599-2.6963	0.2647	622	0.2099	5895	X-RAY DIFFRACTION	100
2.6963-2.7348	0.2649	637	0.2042	5824	X-RAY DIFFRACTION	100
2.7348-2.7756	0.2431	686	0.2052	5854	X-RAY DIFFRACTION	100
2.7756-2.819	0.2759	653	0.2051	5831	X-RAY DIFFRACTION	100
2.819-2.8652	0.2596	662	0.2132	5844	X-RAY DIFFRACTION	100
2.8652-2.9146	0.2714	665	0.2081	5902	X-RAY DIFFRACTION	100
2.9146-2.9676	0.2535	628	0.2008	5826	X-RAY DIFFRACTION	100
2.9676-3.0247	0.2419	625	0.2048	5880	X-RAY DIFFRACTION	100
3.0247-3.0864	0.2524	671	0.2012	5832	X-RAY DIFFRACTION	100
3.0864-3.1535	0.2605	613	0.2188	5902	X-RAY DIFFRACTION	100
3.1535-3.2269	0.253	659	0.1929	5813	X-RAY DIFFRACTION	100
3.2269-3.3075	0.2413	673	0.1974	5822	X-RAY DIFFRACTION	100
3.3075-3.397	0.2344	677	0.1964	5819	X-RAY DIFFRACTION	100
3.397-3.4969	0.2552	629	0.2074	5870	X-RAY DIFFRACTION	100
3.4969-3.6097	0.2378	701	0.1923	5843	X-RAY DIFFRACTION	100
3.6097-3.7387	0.2434	656	0.1985	5868	X-RAY DIFFRACTION	100
3.7387-3.8883	0.2558	663	0.2033	5868	X-RAY DIFFRACTION	100
3.8883-4.0652	0.221	656	0.1949	5831	X-RAY DIFFRACTION	100
4.0652-4.2794	0.221	660	0.1842	5851	X-RAY DIFFRACTION	100
4.2794-4.5474	0.2065	662	0.1816	5845	X-RAY DIFFRACTION	99
4.5474-4.8982	0.224	623	0.1909	5886	X-RAY DIFFRACTION	100
4.8982-5.3906	0.2345	624	0.2072	5920	X-RAY DIFFRACTION	100
5.3906-6.1693	0.2972	640	0.2482	5892	X-RAY DIFFRACTION	100
6.1693-7.7678	0.2603	649	0.2392	5860	X-RAY DIFFRACTION	99
7.7678-49.3617	0.2201	646	0.2136	5770	X-RAY DIFFRACTION	97

-
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