4YS6 | pdb_00004ys6

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTANS (Cphy_1585, TARGET EFI-511156) WITH BOUND BETA-D-GLUCOSE

• PDB DOI: https://doi.org/10.2210/pdb4YS6/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Lachnoclostridium phytofermentans ISDg
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-16 Released: 2015-04-08 
• 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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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM CLOSTRIDIUM PHYTOFERMENTANS (Cphy_1585, TARGET EFI-511156) WITH BOUND BETA-D-GLUCOSE

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: 40.01 kDa 
• Atom Count: 2,701 
• Modeled Residue Count: 324 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative solute-binding component of ABC transporter	A	360	Lachnoclostridium phytofermentans ISDg	Mutation(s): 0  Gene Names: Cphy_1585
UniProt
Find proteins for A9KQP6 (Lachnoclostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg)) Explore A9KQP6  Go to UniProtKB:  A9KQP6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.70 Å
• R-Value Free:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.686	α = 90
b = 80.686	β = 90
c = 170.004	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
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)

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary