5U4Q

1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD.

• PDB DOI: https://doi.org/10.2210/pdb5U4Q/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-05 Released: 2016-12-14 
• Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bishop, B., 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: 1.50 Å
• R-Value Free: 0.211 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD.

Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 78.37 kDa 
• Atom Count: 5,905 
• Modelled Residue Count: 625 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-glucose 4,6-dehydratase	A, B	337	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: rffG_4, rffG_2, SAMEA2273684_00396, SAMEA2273712_05182 EC: 4.2.1.46

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.211 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m35u4q

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.239	α = 90
b = 55.845	β = 93.21
c = 97.318	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary