4RJZ | pdb_00004rjz

Crystal structure of ATU4361 sugar transporter from Agrobacterium fabrum C58, target EFI-510558, an open conformation

• PDB DOI: https://doi.org/10.2210/pdb4RJZ/pdb

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


• Deposited: 2014-10-11 Released: 2014-11-05 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 
  0.165 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Maltoside Transporter ATU4361 from Agrobacterium Fabrum, Target EFI-510558

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 45.59 kDa 
• Atom Count: 3,740 
• Modeled Residue Count: 382 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate binding protein (Sugar)	A	407	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu4361
UniProt
Find proteins for A9CGI0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CGI0  Go to UniProtKB:  A9CGI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-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: 1.17 Å
• R-Value Free:  0.165 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.617	α = 90
b = 41.263	β = 90
c = 70.442	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
ARP/wARP	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Structure summary