3EBT | pdb_00003ebt

Crystal structure of a ntf2-like protein of unknown function (bpss0132) from burkholderia pseudomallei k96243 at 1.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EBT/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Burkholderia pseudomallei K96243
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-28 Released: 2008-09-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.162 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Crystal structure of NTF2-like protein of unknown function (YP_110153.1) from BURKHOLDERIA PSEUDOMALLEI K96243 at 1.30 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)

Macromolecule Content 

• Total Structure Weight: 15.12 kDa 
• Atom Count: 1,347 
• Modeled Residue Count: 132 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized NTF2-like protein	A	132	Burkholderia pseudomallei K96243	Mutation(s): 0  Gene Names: YP_110153.1, BPSS0132
UniProt
Find proteins for Q63P16 (Burkholderia pseudomallei (strain K96243)) Explore Q63P16  Go to UniProtKB:  Q63P16

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	B [auth A], C [auth A]	Unknown ligand

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: 1.30 Å
• R-Value Free:  0.162 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EBT

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.73	α = 90
b = 75.73	β = 90
c = 50.07	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.6: 2025-10-22
  Changes: Structure summary