6J90 | pdb_00006j90

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history. 


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.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B400Salmonella enterica subsp. enterica serovar TyphiMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A2I4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PEG
Query on PEG
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
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), 0.220 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.112α = 90
b = 140.545β = 90
c = 79.105γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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