6J90 | pdb_00006j90

Crystal Structure of GyraseB N-Terminal Domain complex with ATP from Salmonella Typhi at 2.2A Resolution

• PDB DOI: https://doi.org/10.2210/pdb6J90/pdb

• Classification: ISOMERASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-21 Released: 2020-01-22 
• Deposition Author(s): Kaur, G., Sachdeva, E., Tiwari, P., Gupta, D., Ethayathulla, A.S., Kaur, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.217 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of GyraseB N-Terminal Domain complex with ATP from Salmonella Typhi at 2.2A Resolution

Kaur, G., Sachdeva, E., Tiwari, P., Gupta, D., Ethayathulla, A.S., Kaur, P.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.29 kDa 
• Atom Count: 3,408 
• Modeled Residue Count: 390 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	400	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Gene Names: gyrB, STY3943, t3684 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A2I4 (Salmonella typhi) Explore P0A2I4  Go to UniProtKB:  P0A2I4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PEG	F [auth A], G [auth A], H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.217 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.112	α = 90
b = 140.545	β = 90
c = 79.105	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Kaur, G., Sachdeva, E., Tiwari, P., Gupta, D., Ethayathulla, A.S., Kaur, P.

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 2.0: 2020-01-29
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description