5JNF | pdb_00005jnf

Crystal structure of the LgrA initiation module excluding the Asub domain: F-A-delta-sub

• PDB DOI: https://doi.org/10.2210/pdb5JNF/pdb

• Classification: LIGASE
• Organism(s): Brevibacillus parabrevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-29 Released: 2016-10-12 
• Deposition Author(s): Reimer, J.M., Aloise, M.N., Schmeing, T.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.275 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry

Reimer, J.M., Aloise, M.N., Powell, H.R., Schmeing, T.M.

(2016) Acta Crystallogr D Biol Crystallogr 72: 1130-1136

• DOI: https://doi.org/10.1107/S2059798316013504

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 265.34 kDa 
• Atom Count: 18,665 
• Modeled Residue Count: 2,329 
• Deposited Residue Count: 2,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linear gramicidin synthase subunit A	A [auth C], B [auth A], C [auth B], D	587	Brevibacillus parabrevis	Mutation(s): 0  Gene Names: lgrA
UniProt
Find proteins for Q70LM7 (Brevibacillus parabrevis) Explore Q70LM7  Go to UniProtKB:  Q70LM7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	E [auth C], F [auth C], G [auth C], H [auth C], I [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.275 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.311	α = 90
b = 161.311	β = 90
c = 139.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Reimer, J.M., Aloise, M.N., Schmeing, T.M.

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description