3DNX | pdb_00003dnx

SPO1766 protein of unknown function from Silicibacter pomeroyi.

• PDB DOI: https://doi.org/10.2210/pdb3DNX/pdb

• Classification: structural genomics, unknown function
• Organism(s): Ruegeria pomeroyi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-02 Released: 2008-09-02 
• Deposition Author(s): Osipiuk, J., Mulligan, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

X-ray crystal structure of SPO1766 protein of unknown function from Silicibacter pomeroyi.

Osipiuk, J., Mulligan, R., Clancy, S., Joachimiak, A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.55 kDa 
• Atom Count: 1,327 
• Modeled Residue Count: 146 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein SPO1766	A	153	Ruegeria pomeroyi	Mutation(s): 0  Gene Names: SPO1766
UniProt
Find proteins for Q5LSK1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LSK1  Go to UniProtKB:  Q5LSK1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A], C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.892	α = 90
b = 59.892	β = 90
c = 99.868	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Osipiuk, J., Mulligan, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary