4GQA | pdb_00004gqa

Crystal structure of NAD binding oxidoreductase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb4GQA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella variicola 342
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-22 Released: 2012-09-12 
• Deposition Author(s): Osinski, S., Majorek, K.A., Niedzialkowska, E., Osinski, T., Porebski, P.J., Nawar, A., Hammonds, J., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.230 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.186 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of NAD binding oxidoreductase from Klebsiella pneumoniae (CASP Target)

Osinski, S., Majorek, K.A., Niedzialkowska, E., Osinski, T., Porebski, P.J., Nawar, A., Hammonds, J., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 184.83 kDa 
• Atom Count: 12,033 
• Modeled Residue Count: 1,504 
• Deposited Residue Count: 1,648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD binding Oxidoreductase	A, B, C, D	412	Klebsiella variicola 342	Mutation(s): 0  Gene Names: KPK_4084 EC: 1
UniProt
Find proteins for B5Y097 (Klebsiella variicola (strain 342)) Explore B5Y097  Go to UniProtKB:  B5Y097

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth B], G [auth B], H [auth C], I [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	J [auth D], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.230 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.186 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3S88V

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.418	α = 90
b = 113.026	β = 90.54
c = 132.174	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Osinski, S., Majorek, K.A., Niedzialkowska, E., Osinski, T., Porebski, P.J., Nawar, A., Hammonds, J., Hillerich, B., Seidel, R., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary