3GW7

Crystal structure of a metal-dependent phosphohydrolase with conserved HD domain (yedJ) from Escherichia coli in complex with nickel ions. Northeast Structural Genomics Consortium Target ER63

• PDB DOI: https://doi.org/10.2210/pdb3GW7/pdb

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


• Deposited: 2009-03-31 Released: 2009-04-14 
• Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.294 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 

Literature

Crystal structure of a metal-dependent phosphohydrolase with conserved HD domain (yedJ) from Escherichia coli in complex with nickel ions. Northeast Structural Genomics Consortium Target ER63

Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

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)

Macromolecule Content

• Total Structure Weight: 54.5 kDa 
• Atom Count: 3,406 
• Modelled Residue Count: 430 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein yedJ	A, B	239	Escherichia coli K-12	Mutation(s): 0  Gene Names: b1962, JW1945, yedJ
UniProt
Find proteins for P46144 (Escherichia coli (strain K12)) Explore P46144  Go to UniProtKB:  P46144

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.294 
• R-Value Work: 0.260 
• R-Value Observed: 0.263 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.408	α = 90
b = 99.408	β = 90
c = 130.629	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, J., Xiao, R., Cunningham, K., Ma, L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations