2OKQ | pdb_00002okq

Crystal structure of unknown conserved ybaA protein from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb2OKQ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-17 Released: 2007-02-06 
• Deposition Author(s): Minasov, G., Vorontsov, I.I., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Collart, F.R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of unknown conserved ybaA protein from Shigella flexneri

Minasov, G., Vorontsov, I.I., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Collart, F.R., Joachimiak, A., Anderson, W.F.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.2 kDa 
• Atom Count: 2,275 
• Modeled Residue Count: 245 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybaA	A, B	141	Shigella flexneri	Mutation(s): 0  Gene Names: ybaA
UniProt
Find proteins for P0AAQ9 (Shigella flexneri) Explore P0AAQ9  Go to UniProtKB:  P0AAQ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.843	α = 90
b = 61.843	β = 90
c = 137.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Minasov, G., Vorontsov, I.I., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Collart, F.R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations