4GBV | pdb_00004gbv

Crystal Structure of AMP complexes of Porcine Liver Fructose-1,6-bisphosphatase Mutant A54L with 1,2-ethanediol as Cryo-protectant

• PDB DOI: https://doi.org/10.2210/pdb4GBV/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-28 Released: 2013-08-21 
• Deposition Author(s): Honzatko, R.B., Gao, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.243 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Water Structure of the Central Hydrophobic Cavity of Mammalian Fructose-1,6-bisphosphatase: a Potential Thermodynamic Determinant of Allowed Quaternary States

Honzatko, R.B., Gao, Y., Ginder, N.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.35 kDa 
• Atom Count: 2,641 
• Modeled Residue Count: 326 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A	335	Sus scrofa	Mutation(s): 1  Gene Names: FBP, FBP1 EC: 3.1.3.11
UniProt
Find proteins for P00636 (Sus scrofa) Explore P00636  Go to UniProtKB:  P00636

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	F [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
F6P	B [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.243 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.69	α = 90
b = 82.506	β = 90
c = 166.284	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Honzatko, R.B., Gao, Y.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Structure summary