4KQ9

Crystal structure of periplasmic ribose ABC transporter from Conexibacter woesei DSM 14684

• PDB DOI: https://doi.org/10.2210/pdb4KQ9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Conexibacter woesei DSM 14684
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-05-14 Released: 2013-05-29 
• Deposition Author(s): Nocek, B., Chhor, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.234 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal structure of periplasmic ribose ABC transporter from Conexibacter woesei DSM 14684

Nocek, B., Chhor, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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: 31.94 kDa 
• Atom Count: 2,391 
• Modelled Residue Count: 298 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose ABC transporter, substrate binding protein	A	299	Conexibacter woesei DSM 14684	Mutation(s): 1  Gene Names: Cwoe_4347
UniProt
Find proteins for D3F6W3 (Conexibacter woesei (strain DSM 14684 / CCUG 47730 / CIP 108061 / JCM 11494 / NBRC 100937 / ID131577)) Explore D3F6W3  Go to UniProtKB:  D3F6W3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 1.90 Å
• R-Value Free:  0.234 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.469	α = 90
b = 60.536	β = 90
c = 88.898	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
DM	model building
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-29 
Deposition Author(s): Nocek, B., Chhor, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-05-29
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary