6E4B | pdb_00006e4b

The crystal structure of a putative alpha-ribazole-5'-P phosphatase from Escherichia coli str. K-12 substr. MG1655

• PDB DOI: https://doi.org/10.2210/pdb6E4B/pdb

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


• Deposited: 2018-07-17 Released: 2018-09-12 
• Deposition Author(s): Tan, K., Maltseva, N., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of a putative alpha-ribazole-5'-P phosphatase from Escherichia coli str. K-12 substr. MG1655 (CASP target)

Tan, K., Maltseva, N., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.99 kDa 
• Atom Count: 6,334 
• Modeled Residue Count: 807 
• Deposited Residue Count: 908 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylcobalamin/alpha-ribazole phosphatase	A, B, C, D	227	Escherichia coli K-12	Mutation(s): 0  Gene Names: cobC, phpB, b0638, JW0633 EC: 3.1.3.73
UniProt
Find proteins for P52086 (Escherichia coli (strain K12)) Explore P52086  Go to UniProtKB:  P52086

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	G [auth A], H [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A], F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.114	α = 90
b = 53.772	β = 98.09
c = 199.133	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Tan, K., Maltseva, N., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description