5K9F | pdb_00005k9f

Crystal structure of a NIPSNAP domain protein from Burkholderia xenovorans

• PDB DOI: https://doi.org/10.2210/pdb5K9F/pdb

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


• Deposited: 2016-05-31 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: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a NIPSNAP domain protein from Burkholderia xenovorans

Mayclin, S.J., Abendroth, J., Lorimer, D.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: 12.85 kDa 
• Atom Count: 1,016 
• Modeled Residue Count: 103 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NIPSNAP domain protein	A	112	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: Bxe_A1114
UniProt
Find proteins for Q13VQ7 (Paraburkholderia xenovorans (strain LB400)) Explore Q13VQ7  Go to UniProtKB:  Q13VQ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OXM	B [auth A]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35K9F

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.36	α = 90
b = 95.36	β = 90
c = 63.17	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: 2016-06-15 
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: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description