1XVI | pdb_00001xvi

Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12

• PDB DOI: https://doi.org/10.2210/pdb1XVI/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-10-28 Released: 2004-12-14 
• Deposition Author(s): Kim, Y., Joachimiak, A., Cymborowski, M., Skarina, T., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal Structure of YedP, phosphatase-like domain protein from Escherichia coli K12

Kim, Y., Joachimiak, A., Cymborowski, M., Skarina, T., Savchenko, A., Edwards, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.49 kDa 
• Atom Count: 4,166 
• Modeled Residue Count: 466 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative mannosyl-3-phosphoglycerate phosphatase	A, B	275	Escherichia coli K-12	Mutation(s): 0  Gene Names: yedP EC: 3.1.3.70
UniProt
Find proteins for P76329 (Escherichia coli (strain K12)) Explore P76329  Go to UniProtKB:  P76329

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	E [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.783	α = 90
b = 79.975	β = 99.56
c = 75.471	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Kim, Y., Joachimiak, A., Cymborowski, M., Skarina, T., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-12-14
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations