5IXU | pdb_00005ixu

Crystal structure of an uncharacterized NIPSNAP domain protein from Burkholderia xenovorans

• PDB DOI: https://doi.org/10.2210/pdb5IXU/pdb

• Classification: Structural Genomics/Unknown Function
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-23 Released: 2016-03-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an uncharacterized protein from Burkholderia xenovorans

Mayclin, S.J., Delker, S.L., Lorimer, D.D., Edwards, T.E.

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 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 13.84 kDa 
• Atom Count: 836 
• Modeled Residue Count: 102 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	117	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: Bxe_B0070
UniProt
Find proteins for Q13J81 (Paraburkholderia xenovorans (strain LB400)) Explore Q13J81  Go to UniProtKB:  Q13J81

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IXU

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.62	α = 90
b = 94.62	β = 90
c = 94.62	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description