3RYG | pdb_00003ryg

128 hours neutron structure of perdeuterated rubredoxin

• PDB DOI: https://doi.org/10.2210/pdb3RYG/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-11 Released: 2011-12-28 
• Deposition Author(s): Munshi, P., Chung, C.-L., Weiss, K.L., Blakeley, M.P., Myles, D.A.A., Meilleur, F.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.200 (Depositor) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Rapid visualization of hydrogen positions in protein neutron crystallographic structures.

Munshi, P., Chung, S.L., Blakeley, M.P., Weiss, K.L., Myles, D.A., Meilleur, F.

(2012) Acta Crystallogr D Biol Crystallogr 68: 35-41

• PubMed: 22194331 
• DOI: https://doi.org/10.1107/S0907444911048402
• Primary Citation Related Structures: 
  3RYG, 3RZ6, 3RZT, 3SS2


• PubMed Abstract: 
  

  Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.

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Organizational Affiliation: 
• Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.09 kDa 
• Atom Count: 429 
• Modeled Residue Count: 51 
• Deposited Residue Count: 54 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	54	Pyrococcus furiosus DSM 3638	Mutation(s): 0  Gene Names: PF1282, rub
UniProt
Find proteins for P24297 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P24297  Go to UniProtKB:  P24297

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.200 (Depositor) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.37	α = 90
b = 35.34	β = 90
c = 44.11	γ = 90

Software Package:

Software Name	Purpose
LAUEGEN	data collection
PHENIX	refinement
LAUEGEN	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Munshi, P., Chung, C.-L., Weiss, K.L., Blakeley, M.P., Myles, D.A.A., Meilleur, F.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-01-04
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Data collection, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description