4GWU | pdb_00004gwu

Crystal Structure of Fru 2,6-bisphosphate complexes of Porcine Liver Fructose-1,6-bisphosphatase with Filled Central Cavity

• PDB DOI: https://doi.org/10.2210/pdb4GWU/pdb

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


• Deposited: 2012-09-03 Released: 2013-09-04 
• Deposition Author(s): Gao, Y., Honzatko, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Hydrophobic Central Cavity in Fructose-1,6-bisphosphatase is Essential for the Synergism in AMP/Fru 2,6-bisphosphate Inhibition

Gao, Y., Shen, L., Honzatko, R.B.

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: 37.21 kDa 
• Atom Count: 2,437 
• Modeled Residue Count: 307 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A	337	Sus scrofa	Mutation(s): 3  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDP	B [auth A]	2,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 YXWOAJXNVLXPMU-ZXXMMSQZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.999	α = 90
b = 81.221	β = 90
c = 165.058	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: 2013-09-04 
Deposition Author(s): Gao, Y., Honzatko, R.B.

Revision History  

• Version 1.0: 2013-09-04
  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: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary