4RYA | pdb_00004rya

Crystal structure of abc transporter solute binding protein AVI_3567 from AGROBACTERIUM VITIS S4, TARGET EFI-510645, with bound D-mannitol

• PDB DOI: https://doi.org/10.2210/pdb4RYA/pdb

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


• Deposited: 2014-12-13 Released: 2014-12-24 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., 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: 1.50 Å
• R-Value Free: 
  0.168 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Literature

Crystal Structure of Periplasmic Solute-Binding Protein Avi_3567 from Agrobacterium Vitis, Target Efi-510645

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Morisco, L.L., Wasserman, S.R., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C.

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: 46.89 kDa 
• Atom Count: 3,780 
• Modelled Residue Count: 417 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter substrate binding protein (Sorbitol)	A	424	Allorhizobium ampelinum S4	Mutation(s): 0  Gene Names: Avi_3567
UniProt
Find proteins for B9JRF8 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9JRF8  Go to UniProtKB:  B9JRF8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTL	B [auth A]	D-MANNITOL C6 H14 O6 FBPFZTCFMRRESA-KVTDHHQDSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.168 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.413	α = 90
b = 61.256	β = 104.01
c = 65.501	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siedel, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Structure summary
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary