2PVE

NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of Rubredoxin

PDB DOI: https://doi.org/10.2210/pdb2PVE/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Clostridium pasteurianum
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-05-09 Released: 2007-12-18
Deposition Author(s): LeMaster, D.M., Anderson, J.S., Wang, L., Guo, Y., Li, H., Hernandez, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.79 Å
R-Value Free: 0.125
R-Value Observed: 0.112

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin.

Lemaster, D.M., Anderson, J.S., Wang, L., Guo, Y., Li, H., Hernandez, G.

(2007) BMC Struct Biol 7: 81-81

PubMed: 18053245 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-7-81
Primary Citation of Related Structures:
2PVE, 2PVX

PubMed Abstract:
Chimeric hybrids derived from the rubredoxins of Pyrococcus furiosus (Pf) and Clostridium pasteurianum (Cp) provide a robust system for the characterization of protein conformational stability and dynamics in a differential mode. Interchange of the seven nonconserved residues of the metal binding site between the Pf and Cp rubredoxins yields a complementary pair of hybrids, for which the sum of the thermodynamic stabilities is equal to the sum for the parental proteins. Furthermore, the increase in amide hydrogen exchange rates for the hyperthermophile-derived metal binding site hybrid is faithfully mirrored by a corresponding decrease for the complementary hybrid that is derived from the less thermostable rubredoxin, indicating a degree of additivity in the conformational fluctuations that underlie these exchange reactions.

Organizational Affiliation

Wadsworth Center, New York State Department of Health, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York 12201, USA. lemaster@wadsworth.org

Macromolecule Content

Total Structure Weight: 18.67 kDa
Atom Count: 1,613
Modelled Residue Count: 156
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A, B, C	54	Clostridium pasteurianum	Mutation(s): 7
UniProt
Find proteins for P00268 (Clostridium pasteurianum) Explore P00268 Go to UniProtKB: P00268
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00268
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C]	D [auth A], G [auth B], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C]	E [auth A], F [auth A], J [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C]