4YV7

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM MYCOBACTERIUM SMEGMATIS (MSMEI_3018, TARGET EFI-511327) WITH BOUND GLYCEROL

• PDB DOI: https://doi.org/10.2210/pdb4YV7/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-19 Released: 2015-04-01 
• Deposition Author(s): Vetting, M.W., Patskovsky, Y., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, 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)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM MYCOBACTERIUM SMEGMATIS (MSMEI_3018, TARGET EFI-511327) WITH BOUND GLYCEROL

Vetting, M.W., Patskovsky, Y., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.89 kDa 
• Atom Count: 2,214 
• Modelled Residue Count: 288 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A	326	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEI_3018, LJ00_15400 EC: 3.6.3.17
UniProt
Find proteins for I7G195 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7G195  Go to UniProtKB:  I7G195

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.246	α = 90
b = 110.626	β = 90
c = 35.929	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Vetting, M.W., Patskovsky, Y., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, 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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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093342

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary