1OQU

A protein coordinated tri-nuclear Fe complex formed during soaking of crystals of the ribonucleotide reductase R2F protein from Corynebacterium Ammoniagenes

PDB DOI: https://doi.org/10.2210/pdb1OQU/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Corynebacterium ammoniagenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-03-11 Released: 2004-04-20
Deposition Author(s): Hogbom, M., Nordlund, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

A protein carboxylate coordinated oxo-centered tri-nuclear iron complex with possible implications for ferritin mineralization

Hogbom, M., Nordlund, P.

(2004) FEBS Lett 567: 179-182

PubMed: 15178319 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2004.04.068
Primary Citation of Related Structures:
1OQU

PubMed Abstract:
The crystal structure of an oxo-centered tri-nuclear iron complex formed on a protein surface is presented. The cluster forms when crystals of the class Ib ribonucleotide reductase R2 protein from Corynebacterium ammoniagenes are subjected to iron soaking. The tri-iron-oxo complex is coordinated by protein-derived carboxylate ligands arranged in a motif similar to the one found on the inner surface of ferritins and may mimic an early stage in the mineralization of iron in ferritins. In addition, the structure adds to the very limited data on protein-mineral interfaces.

Organizational Affiliation

Department of Biochemistry and Biophysics, Stockholm University Roslagstullsbacken 15, Albanova University Center, Stockholm SE-106 91, Sweden. hogbom@dbb.su.se

Macromolecule Content

Total Structure Weight: 153.11 kDa
Atom Count: 10,489
Modelled Residue Count: 1,190
Deposited Residue Count: 1,316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ribonucleotide reductase subunit R2F	A, B, C, D	329	Corynebacterium ammoniagenes	Mutation(s): 0 EC: 1.17.4.1
UniProt
Find proteins for O69274 (Corynebacterium ammoniagenes) Explore O69274 Go to UniProtKB: O69274
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O69274
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] E [auth A] F [auth A] G [auth A] H [auth A] AA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain J [auth A] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain V [auth C]	BA [auth D], J [auth A], V [auth C]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239 (Depositor), 0.240 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.319	α = 90
b = 91.237	β = 91.459
c = 136.956	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-04-20

Deposition Author(s):

Hogbom, M.

Nordlund, P.

Revision History (Full details and data files)

Version 1.0: 2004-04-20
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Derived calculations