3NQ4 | pdb_00003nq4

30mer structure of Lumazine synthase from Salmonella typhimurium LT2

• PDB DOI: https://doi.org/10.2210/pdb3NQ4/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-29 Released: 2011-06-08 
• Deposition Author(s): Kumar, P., Singh, M., Karthikeyan, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.299 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Lumazine synthase from Salmonella typhimurium LT2

Kumar, P., Singh, M., Karthikeyan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

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

Macromolecule Content 

• Total Structure Weight: 484.51 kDa 
• Atom Count: 33,262 
• Modeled Residue Count: 4,620 
• Deposited Residue Count: 4,680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, AA [auth 1], B, BA [auth 2], C, CA [auth 3], D, DA [auth 4], E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	156	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: ribH, STM0417 EC: 2.5.1.78
UniProt
Find proteins for P66038 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P66038  Go to UniProtKB:  P66038

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AB [auth Q], BB [auth Q], CB [auth Q], DB [auth R], EA [auth A], EB [auth S], FA [auth B], FB [auth U], GA [auth C], GB [auth V], HA [auth C], HB [auth V], IA [auth D], IB [auth X], JA [auth D], JB [auth X], KA [auth E], KB [auth Z], LA [auth F], LB [auth Z], MA [auth F], MB [auth 1], NA [auth G], NB [auth 1], OA [auth H], OB [auth 2], PA [auth H], PB [auth 2], QA [auth H], QB [auth 2], RA [auth J], RB [auth 3], SA [auth K], TA [auth L], UA [auth L], VA [auth M], WA [auth M], XA [auth M], YA [auth N], ZA [auth P]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.299 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.43	α = 90
b = 157.49	β = 91.58
c = 202.788	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CCP4	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Kumar, P., Singh, M., Karthikeyan, S.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-01-23
  Changes: Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description