4X04

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CITROBACTER KOSERI (CKO_04899, TARGET EFI-510094) WITH BOUND D-glucuronate

• PDB DOI: https://doi.org/10.2210/pdb4X04/pdb

• Classification: SOLUTE BINDING PROTEIN
• Organism(s): Citrobacter koseri ATCC BAA-895
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-20 Released: 2014-12-10 
• Deposition Author(s): Yadava, U., 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: 2.50 Å
• R-Value Free: 0.205 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CITROBACTER KOSERI (CKO_04899, TARGET EFI-510094) WITH BOUND D-glucuronate

Yadava, U., 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: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 148.13 kDa 
• Atom Count: 10,452 
• Modelled Residue Count: 1,204 
• Deposited Residue Count: 1,292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
solute binding protein	A, B, C, D	323	Citrobacter koseri ATCC BAA-895	Mutation(s): 0  Gene Names: CKO_04899
UniProt
Find proteins for A8AR30 (Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)) Explore A8AR30  Go to UniProtKB:  A8AR30

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDP	E [auth A], I [auth B], K [auth C], O [auth D]	beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N
CL	F [auth A], G [auth A], J [auth B], L [auth C], M [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	H [auth A], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.205 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175	α = 90
b = 175	β = 90
c = 125.64	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Yadava, U., 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: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2017-09-27
  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: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-11-15
  Changes: Data collection