6X1L

The crystal structure of a functional uncharacterized protein KP1_0663 from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044

PDB DOI: https://doi.org/10.2210/pdb6X1L/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-05-19 Released: 2020-06-03
Deposition Author(s): Tan, K., Wu, R., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.221
R-Value Work: 0.191
R-Value Observed: 0.192

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: 31.88 kDa
Atom Count: 2,149
Modelled Residue Count: 260
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WbbZ protein	A	272	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0 Gene Names: wbbZ
UniProt
Find proteins for A0A0C4KUT2 (Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044) Explore A0A0C4KUT2 Go to UniProtKB: A0A0C4KUT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0C4KUT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.221
R-Value Work: 0.191
R-Value Observed: 0.192
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.202	α = 90
b = 104.202	β = 90
c = 194.534	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2023-06-14
Changes: Database references
Version 1.2: 2024-11-13
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.