4REU

Revelation of Endogenously bound Fe2+ ions in the Crystal Structure of Ferritin from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb4REU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli str. K-12 substr. MDS42
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-09-24 Released: 2014-10-22
Deposition Author(s): Thiruselvam, V., Ponnuswamy, M.N., Kumarevel, T.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.235
R-Value Work: 0.172
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Revelation of endogenously bound Fe(2+) ions in the crystal structure of ferritin from Escherichia coli.

Thiruselvam, V., Sivaraman, P., Kumarevel, T., Ponnuswamy, M.N.

(2014) Biochem Biophys Res Commun 453: 636-641

PubMed: 25305494 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2014.10.007
Primary Citation of Related Structures:
4REU

PubMed Abstract:
Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites. The protein was purified and characterized by MALDI-TOF and N-terminal amino acid sequencing. The crystal belongs to I4 space group and it diffracted up to 2.5Å. The structural analysis suggested that it crystallizes as hexamer and confirmed that it happened to be the first report of endogenously expressed Fe ions incorporated in both the A and B sites, situated in between the helices.

Organizational Affiliation

RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Macromolecule Content

Total Structure Weight: 119.94 kDa
Atom Count: 8,494
Modelled Residue Count: 984
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C, D, E A, B, C, D, E, F	164	Escherichia coli str. K-12 substr. MDS42	Mutation(s): 0 Gene Names: ftn, ECMDS42_1565 EC: 1.16.3.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain OA [auth D] MOL2 format, chain GA [auth C] MOL2 format, chain OA [auth D]	GA [auth C], OA [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain OA [auth D] Interactions & Density Focus chain GA [auth C] Focus chain OA [auth D]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A]	N [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EA [auth C] SDF format, chain EB [auth E] SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JB [auth F] SDF format, chain K [auth A] SDF format, chain KB [auth F] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KB [auth F] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	AB [auth E] BB [auth E] CB [auth E] DB [auth E] EA [auth C] AB [auth E], BB [auth E], CB [auth E], DB [auth E], EA [auth C], EB [auth E], FA [auth C], I [auth A], J [auth A], JB [auth F], K [auth A], KB [auth F], L [auth A], LA [auth D], M [auth A], MA [auth D], NA [auth D], W [auth B], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain JB [auth F] Focus chain K [auth A] Focus chain KB [auth F] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain W [auth B] Focus chain X [auth B]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HB [auth F] SDF format, chain IB [auth F] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E]	CA [auth C] DA [auth C] G [auth A] H [auth A] HB [auth F] CA [auth C], DA [auth C], G [auth A], H [auth A], HB [auth F], IB [auth F], JA [auth D], KA [auth D], U [auth B], V [auth B], YA [auth E], ZA [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth E] Focus chain ZA [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain PB [auth F] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] FB [auth E] GB [auth E] HA [auth C] AA [auth B], BA [auth B], FB [auth E], GB [auth E], HA [auth C], IA [auth C], LB [auth F], MB [auth F], NB [auth F], O [auth A], OB [auth F], P [auth A], PB [auth F], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth A], TA [auth D], UA [auth D], VA [auth D], WA [auth D], XA [auth D], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PB [auth F] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain PA [auth D] MOL2 format, chain PA [auth D]	PA [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain PA [auth D] Interactions & Density Focus chain PA [auth D]