2EBY | pdb_00002eby

Crystal structure of a hypothetical protein from E. Coli

• PDB DOI: https://doi.org/10.2210/pdb2EBY/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-09 Released: 2007-08-14 
• Deposition Author(s): Karthe, P., Kumarevel, T.S., Ebihara, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of a hypothetical protein from E. Coli

Karthe, P., Kumarevel, T.S., Ebihara, S., Kuramitsu, S., Yokoyama, S.

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.

Macromolecule Content 

• Total Structure Weight: 26.76 kDa 
• Atom Count: 1,702 
• Modeled Residue Count: 200 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative HTH-type transcriptional regulator ybaQ	A, B	113	Escherichia coli	Mutation(s): 0  Gene Names: ybaQ
UniProt
Find proteins for P0A9T6 (Escherichia coli (strain K12)) Explore P0A9T6  Go to UniProtKB:  P0A9T6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.793	α = 90
b = 89.793	β = 90
c = 54.25	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-14 
Deposition Author(s): Karthe, P., Kumarevel, T.S., Ebihara, A., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-08-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations