6NBG | pdb_00006nbg

2.05 Angstrom Resolution Crystal Structure of Hypothetical Protein KP1_5497 from Klebsiella pneumoniae.

PDB DOI: https://doi.org/10.2210/pdb6NBG/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-07 Released: 2018-12-19
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.231 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.202 (Depositor)

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 PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 161.28 kDa
Atom Count: 11,887
Modeled Residue Count: 1,442
Deposited Residue Count: 1,452
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate deaminase	A, B, C, D, E A, B, C, D, E, F	242	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: nagB_2, DM059_30720, SAMEA4364603_04465 EC: 3.5.99.6
UniProt
Find proteins for A0A332QZQ2 (Klebsiella pneumoniae) Explore A0A332QZQ2 Go to UniProtKB: A0A332QZQ2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A332QZQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth E] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth F]	G [auth A] H [auth B] J [auth D] K [auth D] L [auth E] G [auth A], H [auth B], J [auth D], K [auth D], L [auth E], M [auth E], N [auth F], O [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.231 (Depositor), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.202 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36nbg

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.482	α = 90
b = 123.806	β = 90
c = 299.664	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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, Refinement description
Version 1.2: 2024-10-09
Changes: Data collection, Structure summary