5KAK | pdb_00005kak

Crystal structure of an uncharacterized NIPSNAP-like domain protein from Burkholderia xenovorans

• PDB DOI: https://doi.org/10.2210/pdb5KAK/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2016-06-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Putative uncharacterized protein from Burkholderia xenovorans LB400

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Delker, S.L., Mayclin, S.J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 121.5 kDa 
• Atom Count: 9,050 
• Modeled Residue Count: 945 
• Deposited Residue Count: 1,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F, G, H	126	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: Bxe_B2134
UniProt
Find proteins for Q13PY7 (Paraburkholderia xenovorans (strain LB400)) Explore Q13PY7  Go to UniProtKB:  Q13PY7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth C], K [auth C], L [auth D], M [auth F], N [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.63	α = 90
b = 70.83	β = 98.62
c = 109.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Data collection
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description