3ZBH | pdb_00003zbh

Geobacillus thermodenitrificans EsxA crystal form I

• PDB DOI: https://doi.org/10.2210/pdb3ZBH/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Geobacillus thermodenitrificans
• Mutation(s): No 


• Deposited: 2012-11-09 Released: 2012-11-21 
• Deposition Author(s): Ng, W.M., Zoltner, M., Palmer, T., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Homodimeric Esat-6-Family Proteins Esxa and Esxb from Geobacillus Thermodenitrificans

Zoltner, M., Ng, W.M., Palmer, T., Hunter, W.N.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.86 kDa 
• Atom Count: 6,328 
• Modeled Residue Count: 734 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESXA	A, B, C, D, E, F, G, H	99	Geobacillus thermodenitrificans	Mutation(s): 0
UniProt
Find proteins for A4IKE4 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IKE4  Go to UniProtKB:  A4IKE4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	J [auth A], K [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	I [auth A], L [auth B], M [auth B], N [auth B], O [auth C], P [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.948	α = 90
b = 58.641	β = 112.36
c = 85.219	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Ng, W.M., Zoltner, M., Palmer, T., Hunter, W.N.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description