6ALL | pdb_00006all

Crystal structure of a predicted ferric/iron (III) hydroxymate siderophore substrate binding protein from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb6ALL/pdb

• Classification: METAL TRANSPORT
• Organism(s): Bacillus anthracis str. 'Ames Ancestor
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-08 Released: 2017-08-16 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a predicted ferric/iron (III) hydroxymate siderophore substrate binding protein from Bacillus anthracis

Stogios, P.J.

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)

Macromolecule Content 

• Total Structure Weight: 74.16 kDa 
• Atom Count: 4,564 
• Modeled Residue Count: 575 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe(3+)-citrate-binding protein yfmC	A, B	324	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0  Gene Names: yfmC, GBAA_4766, BASH2_01198
UniProt
Find proteins for Q81L65 (Bacillus anthracis) Explore Q81L65  Go to UniProtKB:  Q81L65

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	C [auth A], D [auth B], E [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36all

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.505	α = 90
b = 125.505	β = 90
c = 60.262	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Skarina, T., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description