5HQJ

Crystal structure of ABC transporter Solute Binding Protein B1G1H7 from Burkholderia graminis C4D1M, target EFI-511179, in complex with D-arabinose

• PDB DOI: https://doi.org/10.2210/pdb5HQJ/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Paraburkholderia graminis C4D1M
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-21 Released: 2016-03-02 
• Deposition Author(s): Roth, Y., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.254 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Crystal structure of ABC transporter Solute Binding Protein B1G1H7 from Burkholderia graminis C4D1M, target EFI-511179, in complex with D-arabinose

Roth, Y., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., 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: 33.92 kDa 
• Atom Count: 2,468 
• Modelled Residue Count: 289 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A	311	Paraburkholderia graminis C4D1M	Mutation(s): 0  Gene Names: BgramDRAFT_3172
UniProt
Find proteins for B1G1H7 (Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)) Explore B1G1H7  Go to UniProtKB:  B1G1H7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
64K	B [auth A]	alpha-D-arabinopyranose C5 H10 O5 SRBFZHDQGSBBOR-MBMOQRBOSA-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: 1.55 Å
• R-Value Free: 0.254 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.094	α = 90
b = 37.403	β = 113.61
c = 62.429	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Roth, Y., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary