4G9B

Crystal structure of beta-phosphoglucomutase homolog from escherichia coli, target efi-501172, with bound mg, open lid

• PDB DOI: https://doi.org/10.2210/pdb4G9B/pdb

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


• Deposited: 2012-07-23 Released: 2012-08-15 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Crystal structure of beta-phosphoglucomutase homolog from escherichia coli, target efi-501172, with bound mg, open lid

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 27.16 kDa 
• Atom Count: 1,989 
• Modelled Residue Count: 227 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A	243	Escherichia coli K-12	Mutation(s): 0  Gene Names: ycjU, b1317, JW1310 EC: 5.4.2.6
UniProt
Find proteins for P77366 (Escherichia coli (strain K12)) Explore P77366  Go to UniProtKB:  P77366

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	J [auth A]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.168	α = 90
b = 129.168	β = 90
c = 85.766	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Dunaway-Mariano, D., Allen, K.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description