4ONY | pdb_00004ony

Crystal structure of a ABC transporter, periplasmic substrate-binding protein from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb4ONY/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Brucella melitensis ATCC 23457
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-29 Released: 2014-06-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a ABC transporter, periplasmic substrate-binding protein from Brucella melitensis

Abendroth, J., Clifton, M.C., Lorimer, D., Edwards, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 135.57 kDa 
• Atom Count: 10,575 
• Modeled Residue Count: 1,166 
• Deposited Residue Count: 1,190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular solute-binding protein family 5	A, B	595	Brucella melitensis ATCC 23457	Mutation(s): 0  Gene Names: BMEA_B0549
UniProt
Find proteins for C0RL96 (Brucella melitensis biotype 2 (strain ATCC 23457)) Explore C0RL96  Go to UniProtKB:  C0RL96

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4G	D [auth A], G [auth B]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ONY

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.56	α = 90
b = 124.32	β = 90
c = 172.19	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description