4ZJP

Structure of an ABC-Transporter Solute Binding Protein (SBP_IPR025997) from Actinobacillus Succinogenes (Asuc_0197, TARGET EFI-511067) with bound beta-D-ribopyranose

• PDB DOI:  https://doi.org/10.2210/pdb4ZJP/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Actinobacillus succinogenes 130Z
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-29 Released: 2015-05-20 
• Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Glenn, A.S., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., 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: 1.63 Å
• R-Value Free: 0.185 
• R-Value Work: 0.141 
• R-Value Observed: 0.144 

Literature

Structure of an ABC-Transporter Solute Binding Protein (SBP_IPR025997) from Actinobacillus Succinogenes (Asuc_0197, TARGET EFI-511067) with bound beta-D-ribopyranose

Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Glenn, A.S., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., 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: 31.04 kDa 
• Atom Count: 2,392 
• Modelled Residue Count: 270 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monosaccharide-transporting ATPase	A	292	Actinobacillus succinogenes 130Z	Mutation(s): 0  Gene Names: Asuc_0197 EC: 3.6.3.17

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIP	B [auth A]	beta-D-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-TXICZTDVSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.63 Å
• R-Value Free: 0.185 
• R-Value Work: 0.141 
• R-Value Observed: 0.144 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.261	α = 95.2
b = 37.416	β = 101.03
c = 48.165	γ = 97.09

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Glenn, A.S., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary