Evidence map›Paper›PMID 22457093›Full record

ArticlePhotosynthesis research2012

Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum.

Dale E Tronrud, James P Allen

Abstract read
In one paragraph

Article in Photosynthesis research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Models of protein-ligand crystal structures: trust, but verify.Journal of computer-aided molecular design · 2015
    Article
  3. The solvent component of macromolecular crystals.Acta crystallographica. Section D, Biological crystallography · 2015
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Dale E TronrudDepartment of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA. tronrudd@science.oregonstate.edu
James P Allen

Funding

Improving Modeling by Learning from Details of High Accuracy Protein StructuresR01GM083136 · NIGMS · OREGON STATE UNIVERSITY · PI KARPLUS, PAUL ANDREW · 2008 to 2015
$1.7M
NIGMS NIH HHS R01 GM083136
6 · The paper itself

Abstract

The Fenna-Matthews-Olson antenna protein from the green bacterium Pelodictyon phaeum mediates the energy transfer from a peripheral antenna complex to the membrane-bound reaction center. The three-dimensional structure of this protein has been previously modeled using X-ray diffraction to a resolution limit of 2.0 Å, with R (work) and R (free) values of 16.6 and 19.9%, respectively (Larson et al., Photosynth Res 107:139-150, 2011). This model shows the protein as consisting of β-sheets surrounding several bacteriochlorophyll cofactors. While most of the model clearly matches the electron density maps, in this paper we re-examine the electron density for a specific feature, namely the eighth bacteriochlorophyll a cofactor. This electron density is now interpreted as arising primarily from the end of an otherwise disordered polyethylene glycol molecule. Additional electron density is present but the density is weak and cannot be unambiguously assigned. The new model has R (work) and R (free) values of 16.2 and 19.0%, respectively.

Indexed as

ElectronsBacterial ProteinsBacteriochlorophyll ABinding SitesChlorobiCoenzymesEnergy TransferLight-Harvesting Protein ComplexesModels, MolecularPolyethylene GlycolsProtein Structure, SecondaryBacterial ProteinsBacteriochlorophyll ACoenzymesFMO bacteriochlorophyll protein, BacteriaLight-Harvesting Protein ComplexesPolyethylene Glycols

Identifiers

PMID22457093
PMCPMC3732665

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.