4PF6

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM ROSEOBACTER DENITRIFICANS (RD1_0742, TARGET EFI-510239) WITH BOUND 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID (KDO)

• PDB DOI: https://doi.org/10.2210/pdb4PF6/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Roseobacter denitrificans OCh 114
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-28 Released: 2014-05-14 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., 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: 1.75 Å
• R-Value Free: 0.162 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

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: 37.25 kDa 
• Atom Count: 2,857 
• Modelled Residue Count: 305 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4-dicarboxylate-binding protein	A	330	Roseobacter denitrificans OCh 114	Mutation(s): 0  Gene Names: RD1_0742
UniProt
Find proteins for Q16C67 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114)) Explore Q16C67  Go to UniProtKB:  Q16C67

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KDO	B [auth A]	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid C8 H14 O8 NNLZBVFSCVTSLA-HXUQBWEZSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.75 Å
• R-Value Free: 0.162 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.527	α = 90
b = 100.527	β = 90
c = 159.213	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Stead, M., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., 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: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2015-10-07
  Changes: Experimental preparation
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references, Structure summary