4NE4 | pdb_00004ne4

Crystal structure of ABC transporter substrate binding protein ProX from Agrobacterium tumefaciens cocrystalized with BTB

• PDB DOI: https://doi.org/10.2210/pdb4NE4/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-28 Released: 2013-11-27 
• Deposition Author(s): Tkaczuk, K.L., Nicholls, R., Kagan, O., Chruszcz, M., Domagalski, M.J., Savchenko, A., Joachimiak, A., Murshudov, G., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.186 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal structure of ABC transporter substrate binding protein ProX from Agrobacterium tumefaciens cocrystalized with BTB

Nicholls, R., Tkaczuk, K.L., Kagan, O., Chruszcz, M., Domagalski, M.J., Savchenko, A., Joachimiak, A., Murshudov, G., Minor, W., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 30.85 kDa 
• Atom Count: 2,632 
• Modeled Residue Count: 281 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate binding protein (Proline/glycine/betaine)	A	286	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu0199
UniProt
Find proteins for A9CKK7 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CKK7  Go to UniProtKB:  A9CKK7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	B [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.186 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.888	α = 90
b = 64.388	β = 90
c = 100.746	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Tkaczuk, K.L., Nicholls, R., Kagan, O., Chruszcz, M., Domagalski, M.J., Savchenko, A., Joachimiak, A., Murshudov, G., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-27
  Changes: Data collection, Structure summary