1TXL | pdb_00001txl

Crystal structure of metal-binding protein yodA from E. coli, Pfam DUF149

• PDB DOI: https://doi.org/10.2210/pdb1TXL/pdb

• Classification: structural genomics, unknown function
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-05 Released: 2004-07-20 
• Deposition Author(s): Eswaramoorthy, S., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.252 (Depositor) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of a hypothetical protein yodA

Eswaramoorthy, S., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.73 kDa 
• Atom Count: 1,762 
• Modeled Residue Count: 188 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-binding protein yodA	A	215	Escherichia coli	Mutation(s): 0  Gene Names: YODA, B1973
UniProt
Find proteins for P76344 (Escherichia coli (strain K12)) Explore P76344  Go to UniProtKB:  P76344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.252 (Depositor) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.24	α = 90
b = 65.24	β = 117.66
c = 41.34	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SCALEPACK	data scaling
SOLVE	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-20 
Deposition Author(s): Eswaramoorthy, S., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-07-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary