6DT3 | pdb_00006dt3

1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES

• PDB DOI: https://doi.org/10.2210/pdb6DT3/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-15 Released: 2018-06-27 
• Deposition Author(s): Minasov, G., Shuvalova, L., Pshenychnyi, S., Endres, M., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.

Inniss, N.L., Kochan, T.J., Minasov, G., Wawrzak, Z., Chang, C., Tan, K., Shuvalova, L., Kiryukhina, O., Pshenychnyi, S., Wu, R., Dubrovska, I., Babnigg, G., Endres, M., Anderson, W.F., Hauser, A.R., Joachimiak, A., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0101322-e0101322

• PubMed: 36695589 
• DOI: https://doi.org/10.1128/mra.01013-22
• Primary Citation of Related Structures:  
  6DT3, 6DUX, 6DVV, 6DXN, 6E85, 6NAU, 6NBG, 6NDI, 6WN5, 6WN8, 6X1L, 7RJJ, 7TL5, 7TZP


• PubMed Abstract: 
  

  Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team (LS-CAT), Northwestern University, Argonne, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.
Recombinant Protein Production Core, Northwestern University, Evanston, Illinois, USA.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

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)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 33.55 kDa 
• Atom Count: 2,904 
• Modeled Residue Count: 287 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside triphosphatase NudI	A, B	144	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0  Gene Names: nudI, B1727_21840 EC: 3.6.1.9 (PDB Primary Data), 3.6.1.12 (PDB Primary Data), 3.6.1 (PDB Primary Data), 3.6.1.23 (PDB Primary Data)
UniProt
Find proteins for A0A1W1Q5B1 (Klebsiella pneumoniae) Explore A0A1W1Q5B1  Go to UniProtKB:  A0A1W1Q5B1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

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: 1.20 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36dt3

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.14	α = 77.07
b = 39.346	β = 80.74
c = 56.294	γ = 86.2

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: 2018-06-27 
Deposition Author(s): Minasov, G., Shuvalova, L., Pshenychnyi, S., Endres, M., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary