3KE2

CRYSTAL STRUCTURE OF a DUF2131 family protein (SAMA_2911) FROM SHEWANELLA AMAZONENSIS SB2B AT 2.50 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3KE2/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Shewanella amazonensis SB2B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-23 Released: 2009-11-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Crystal structure of STRUCTURAL GENOMICS, UNKNOWN FUNCTION (YP_928783.1) from SHEWANELLA AMAZONENSIS SB2B at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly Evidence: light scattering, gel filtration

Biological Assembly 2  

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

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

Biological Assembly Evidence: light scattering, gel filtration

Macromolecule Content

• Total Structure Weight: 39.32 kDa 
• Atom Count: 2,448 
• Modelled Residue Count: 296 
• Deposited Residue Count: 351 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein YP_928783.1	A, B, C	117	Shewanella amazonensis SB2B	Mutation(s): 0  Gene Names: Sama_2911
UniProt
Find proteins for A1S9Q7 (Shewanella amazonensis (strain ATCC BAA-1098 / SB2B)) Explore A1S9Q7  Go to UniProtKB:  A1S9Q7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth C], H [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	D [auth A], E [auth B], F [auth C]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M33KE2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.479	α = 90
b = 100.509	β = 90
c = 114.583	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations