3F4W | pdb_00003f4w

The 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb3F4W/pdb

• Classification: SYNTHASE, LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-03 Released: 2008-11-25 
• Deposition Author(s): Vijayalakshmi, J., Woodard, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

The 1.65A Crystal Structure of 3-hexulose-6-phosphate synthase from Salmonella typhimurium

Vijayalakshmi, J., Meredith, T.C., Woodard, R.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: 45.69 kDa 
• Atom Count: 3,694 
• Modeled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hexulose 6 phosphate synthase	A, B	211	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: HUMPS, STM2755 EC: 4.1.2 (PDB Primary Data), 4.1.2.43 (UniProt), 4.1.1.85 (UniProt)
UniProt
Find proteins for Q8ZMP9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZMP9  Go to UniProtKB:  Q8ZMP9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	C [auth A], D [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.971	α = 90
b = 108.971	β = 90
c = 36.702	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Vijayalakshmi, J., Woodard, R.W.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description