4MHF

Crystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Glucuronate, space group P21

• PDB DOI: https://doi.org/10.2210/pdb4MHF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Polaromonas sp. JS666
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-29 Released: 2013-09-18 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Zhao, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Jacobson, M.P., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.145 
• R-Value Work: 0.117 
• R-Value Observed: 0.119 

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: 37.11 kDa 
• Atom Count: 2,840 
• Modelled Residue Count: 301 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP dicarboxylate transporter, DctP subunit	A	337	Polaromonas sp. JS666	Mutation(s): 0  Gene Names: Bpro_3107
UniProt
Find proteins for Q128M1 (Polaromonas sp. (strain JS666 / ATCC BAA-500)) Explore Q128M1  Go to UniProtKB:  Q128M1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCU	C [auth A]	alpha-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-WAXACMCWSA-N
BDP	B [auth A]	beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.145 
• R-Value Work: 0.117 
• R-Value Observed: 0.119 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.48	α = 90
b = 45.96	β = 97.66
c = 63.98	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Zhao, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Jacobson, M.P., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary