3NTL | pdb_00003ntl

Crystal Structure of Glucose-1-phosphatase (AgpE) from Enterobacter cloacae

• PDB DOI: https://doi.org/10.2210/pdb3NTL/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-07-05 Released: 2011-07-27 
• Deposition Author(s): Grishkovskaya, I., Hoehne, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Glucose-1-phosphatase (AgpE) from Enterobacter cloacae

Grishkovskaya, I., Herter, T., Wessner, H., Borriss, R., Hoehne, W.

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: 90.65 kDa 
• Atom Count: 6,947 
• Modeled Residue Count: 775 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid glucose-1-phosphate phosphatase	A, B	398	Enterobacter cloacae	Mutation(s): 1  Gene Names: agp
UniProt
Find proteins for Q6EV19 (Enterobacter cloacae) Explore Q6EV19  Go to UniProtKB:  Q6EV19

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	C [auth A], E [auth B]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.079	α = 90
b = 151.079	β = 90
c = 86.644	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Grishkovskaya, I., Hoehne, W.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary