6NAU | pdb_00006nau

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

PDB DOI: https://doi.org/10.2210/pdb6NAU/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-12-06 Released: 2018-12-19
Deposition Author(s): Minasov, G., Shuvalova, L., Pshenychnyi, S., Dubrovska, I., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.156 (Depositor), 0.166 (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

PubMed: 36695589 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/mra.01013-22
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 110.77 kDa
Atom Count: 10,330
Modeled Residue Count: 1,002
Deposited Residue Count: 1,002
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconolactonase	A, B, C	334	Klebsiella pneumoniae subsp. pneumoniae	Mutation(s): 0 Gene Names: ybhE, pgl, NCTC9504_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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6T6J6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain K [auth C] Focus chain L [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain F [auth A]	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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]