6NAU | pdb_00006nau

1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolactonase from Klebsiella pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.156 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.126 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.127 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation
    • Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconolactonase
A, B, C
334Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: ybhEpglNCTC9504_04578
EC: 3.1.1.31
UniProt
Find proteins for A6T6J6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6T6J6 
Go to UniProtKB:  A6T6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6T6J6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth C],
L [auth C]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth B]
J [auth B]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
M [auth C],
N [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.156 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.126 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.127 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.745α = 90
b = 184.745β = 90
c = 48.761γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description