4YBA | pdb_00004yba

The structure of the C.Kpn2I controller protein

• PDB DOI: https://doi.org/10.2210/pdb4YBA/pdb

• Classification: GENE REGULATION
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-18 Released: 2016-03-02 
• Deposition Author(s): Shevtsov, M.B., Martin, R.N., Swiderska, A., McGeehan, G.E., Kneale, G.G.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

The structure of the C.kpn2I controller protein

Shevtsov, M.B., Swiderska, A., Martin, R.N., McGeehan, G.E., Kneale, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.97 kDa 
• Atom Count: 1,328 
• Modeled Residue Count: 155 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein C	A, B	99	Klebsiella pneumoniae	Mutation(s): 0
UniProt
Find proteins for Q93K36 (Klebsiella pneumoniae) Explore Q93K36  Go to UniProtKB:  Q93K36

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.89	α = 90
b = 44.73	β = 90
c = 109.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Shevtsov, M.B., Martin, R.N., Swiderska, A., McGeehan, G.E., Kneale, G.G.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/H00680X/1

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description