PDBsum entry 3kyv

Electron transport

PDB id: 3kyv

Contents

Protein chain

54 a.a. *

Ligands

DOD ×96

Metals

_FE

* Residue conservation analysis

PDB id:

3kyv

Name:

Electron transport

Title:

Denovo x-ray crystal structure determination of h-labeled perdeuterated rubredoxin at 100k

Structure:

Rubredoxin. Chain: a. Synonym: rd. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Gene: rub, pf1282. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.10Å R-factor: 0.129 R-free: 0.147

Authors:

A.S.Gardberg

Key ref:

A.S.Gardberg et al. (2010). Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography. Acta Crystallogr D Biol Crystallogr, 66, 558-567. PubMed id: 20445231

Date:

07-Dec-09 Release date: 28-Apr-10

Protein chain

P24297  (RUBR_PYRFU) -  Rubredoxin from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 54 a.a.

Struc: 54 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Acta Crystallogr D Biol Crystallogr 66:558-567 (2010)

PubMed id: 20445231

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

A.S.Gardberg, A.R.Del Castillo, K.L.Weiss, F.Meilleur, M.P.Blakeley, D.A.Myles.

ABSTRACT

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.