3IPF | pdb_00003ipf

Crystal structure of the Q251Q8_DESHY protein from Desulfitobacterium hafniense. Northeast Structural Genomics Consortium Target DhR8c.

• PDB DOI: https://doi.org/10.2210/pdb3IPF/pdb

• Classification: structural genomics, unknown function
• Organism(s): Desulfitobacterium hafniense Y51
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-17 Released: 2009-09-15 
• Deposition Author(s): Vorobiev, S.M., Chen, Y., Seetharaman, J., Janjua, H., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Andre, I., Rossi, P., Kennedy, M., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the Q251Q8_DESHY protein from Desulfitobacterium hafniense.

Vorobiev, S.M., Chen, Y., Seetharaman, J., Janjua, H., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Andre, I., Rossi, P., Kennedy, M., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, assay for oligomerization

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16 kDa 
• Atom Count: 1,103 
• Modeled Residue Count: 134 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	71	Desulfitobacterium hafniense Y51	Mutation(s): 0  Gene Names: DSY0195
UniProt
Find proteins for Q251Q8 (Desulfitobacterium hafniense (strain Y51)) Explore Q251Q8  Go to UniProtKB:  Q251Q8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.796	α = 90
b = 69.796	β = 90
c = 132.161	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Vorobiev, S.M., Chen, Y., Seetharaman, J., Janjua, H., Xiao, R., Ciccosanti, C., Wang, H., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Andre, I., Rossi, P., Kennedy, M., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description