4OVR

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM XANTHOBACTER AUTOTROPHICUS PY2, TARGET EFI-510329, WITH BOUND BETA-D-GALACTURONATE

• PDB DOI: https://doi.org/10.2210/pdb4OVR/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Xanthobacter autotrophicus Py2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-12 Released: 2014-01-22 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., 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: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.43 kDa 
• Atom Count: 5,460 
• Modelled Residue Count: 596 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP dicarboxylate transporter, DctP subunit	A, B	322	Xanthobacter autotrophicus Py2	Mutation(s): 0  Gene Names: Xaut_3368
UniProt
Find proteins for A7IKQ4 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7IKQ4  Go to UniProtKB:  A7IKQ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTR	E [auth A], F [auth B]	beta-D-galactopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-DTEWXJGMSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.314	α = 90
b = 111.362	β = 90
c = 59.546	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., 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: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2015-02-25
  Changes: Database references
• Version 1.3: 2015-10-14
  Changes: Non-polymer description
• Version 1.4: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 2.0: 2019-12-25
  Changes: Atomic model, Author supporting evidence, Data collection
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary