1LH0

Crystal Structure of Salmonella typhimurium OMP Synthase in Complex with MGPRPP and Orotate

• PDB DOI: https://doi.org/10.2210/pdb1LH0/pdb

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


• Deposited: 2002-04-16 Released: 2002-05-08 
• Deposition Author(s): Fedorov, A.A., Panneerselvam, K., Shi, W., Grubmeyer, C., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• R-Value Observed: 0.210 

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: 47.91 kDa 
• Atom Count: 3,596 
• Modelled Residue Count: 419 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OMP synthase	A, B	213	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  EC: 2.4.2.10
UniProt
Find proteins for P08870 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P08870  Go to UniProtKB:  P08870

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRP	F [auth B]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N
ORO	C [auth A], E [auth B]	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• R-Value Observed: 0.210 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.57	α = 90
b = 154.23	β = 90
c = 52.6	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-08 
Deposition Author(s): Fedorov, A.A., Panneerselvam, K., Shi, W., Grubmeyer, C., Almo, S.C.

Revision History  

• Version 1.0: 2002-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-17
  Changes: Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary