5U9C

1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica

• PDB DOI: https://doi.org/10.2210/pdb5U9C/pdb

• Classification: HYDROLASE,OXIDOREDUCTASE
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-15 Released: 2016-12-28 
• Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Olphie, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.191 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica.

Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Olphie, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 194.35 kDa 
• Atom Count: 15,720 
• Modelled Residue Count: 1,732 
• Deposited Residue Count: 1,752 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose Reductase	A, B, C, D, E, F	292	Yersinia enterocolitica	Mutation(s): 0  Gene Names: wbbW
UniProt
Find proteins for Q56905 (Yersinia enterocolitica) Explore Q56905  Go to UniProtKB:  Q56905

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	M [auth D], N [auth D], P [auth E], Q [auth F]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
BDF	G [auth A], K [auth C], L [auth C]	beta-D-fructopyranose C6 H12 O6 LKDRXBCSQODPBY-ARQDHWQXSA-N
MLT	J [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
TRS	R [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
IMD	H [auth A], I [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CL	O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	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: 0.191 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: I 2 2 2
• Diffraction Data: https://doi.org/10.18430/M35U9C

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.445	α = 90
b = 184.871	β = 90
c = 187.017	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Olphie, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary