4RWE | pdb_00004rwe

The crystal structure of a sugar-binding transport protein from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb4RWE/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Yersinia pestis A1122
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-03 Released: 2014-12-31 
• Deposition Author(s): Tan, K., Zhou, M., Clancy, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

The crystal structure of a sugar-binding transport protein from Yersinia pestis CO92

Tan, K., Zhou, M., Clancy, S., Anderson, W.F., Joachimiak, A.

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: 31.01 kDa 
• Atom Count: 2,370 
• Modeled Residue Count: 287 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar-binding transport protein	A	292	Yersinia pestis A1122	Mutation(s): 0  Gene Names: A1122_06015, Yersinia pestis
UniProt
Find proteins for A0A0H2W6Z9 (Yersinia pestis) Explore A0A0H2W6Z9  Go to UniProtKB:  A0A0H2W6Z9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-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	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:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34rwe

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.94	α = 90
b = 59.94	β = 90
c = 169.926	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Tan, K., Zhou, M., Clancy, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary