6NPO | pdb_00006npo

Crystal structure of oligopeptide ABC transporter from Bacillus anthracis str. Ames (substrate-binding domain)

• PDB DOI: https://doi.org/10.2210/pdb6NPO/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacillus anthracis, Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-18 Released: 2019-02-06 
• Deposition Author(s): Michalska, K., Maltseva, N., Endres, M., Joachimiak, A., 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: 2.40 Å
• R-Value Free: 
  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of oligopeptide ABC transporter from Bacillus anthracis str. Ames (substrate-binding domain)

Michalska, K., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.35 kDa 
• Atom Count: 4,241 
• Modeled Residue Count: 522 
• Deposited Residue Count: 550 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide ABC transporter, oligopeptide-binding protein	A	546	Bacillus anthracis	Mutation(s): 0  Gene Names: BA_3645, GBAA_3645
UniProt
Find proteins for Q81YA8 (Bacillus anthracis) Explore Q81YA8  Go to UniProtKB:  Q81YA8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown peptide ligand	B [auth C]	4	Escherichia coli BL21(DE3)	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
UNK	B [auth C]	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.254 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36npo

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.542	α = 90
b = 54.9	β = 106.21
c = 82.917	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Michalska, K., Maltseva, N., Endres, M., Joachimiak, A., 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	HHSN272201700060C

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary