2Q2L

Crystal Structure of Superoxide Dismutase from P. atrosanguina

PDB DOI: https://doi.org/10.2210/pdb2Q2L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Potentilla atrosanguinea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-05-29 Released: 2008-03-25
Deposition Author(s): Manickam, Y., Gill, J., Mishra, P.C., Sharma, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.234
R-Value Work: 0.167

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and completeness on structure solution

Yogavel, M., Gill, J., Mishra, P.C., Sharma, A.

(2007) Acta Crystallogr D Biol Crystallogr 63: 931-934

PubMed: 17642520 Search on PubMed
DOI: https://doi.org/10.1107/S0907444907029174
Primary Citation of Related Structures:
2Q2L

PubMed Abstract:
Superoxide dismutase (SOD) from Potentilla atrosanguinea (Wall. ex. Lehm.) was crystallized using 20% PEG 3350 and 0.2 M ammonium iodide and diffraction data were collected to 2.36 A resolution using an in-house Cu Kalpha X-ray source. Analyses show that data with a redundancy of 3.2 were sufficient to determine the structure by the SAD technique using the iodine anomalous signal. This redundancy is lower than that in previous cases in which protein structures were determined using iodines for phasing and in-house copper X-ray sources. Cocrystallization of proteins with halide salts such as ammonium iodide in combination with copper-anode X-ray radiation can therefore serve as a powerful and easy avenue for structure solution.

Organizational Affiliation

Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.

Macromolecule Content

Total Structure Weight: 31.83 kDa
Atom Count: 2,399
Modelled Residue Count: 304
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide Dismutase	A, B	152	Potentilla atrosanguinea	Mutation(s): 0 EC: 1.15.1.1
UniProt
Find proteins for B2CP37 (Potentilla atrosanguinea) Explore B2CP37 Go to UniProtKB: B2CP37
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2CP37
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain D [auth A] 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] MOL2 format, chain D [auth A] 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]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], 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]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth A] 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] Interactions & Density Focus chain D [auth A] 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]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]