4WUT | pdb_00004wut

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS (Avi_5133, TARGET EFI-511220) WITH BOUND D-FUCOSE

• PDB DOI: https://doi.org/10.2210/pdb4WUT/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Allorhizobium ampelinum S4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-03 Released: 2014-12-17 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., 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: 1.50 Å
• R-Value Free: 
  0.207 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS (Avi_5133, TARGET EFI-511220) WITH BOUND D-FUCOSE

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., 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.

Macromolecule Content 

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,558 
• Modeled Residue Count: 290 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate binding protein (Ribose)	A	313	Allorhizobium ampelinum S4	Mutation(s): 0  Gene Names: rbsB, Avi_5133
UniProt
Find proteins for B9K0B2 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9K0B2  Go to UniProtKB:  B9K0B2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FCB	E [auth A]	beta-D-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-FPRJBGLDSA-N
CA	F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	B [auth A], C [auth A], D [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: 1.50 Å
• R-Value Free:  0.207 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.188	α = 90
b = 69.367	β = 90
c = 92.434	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., 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: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary