6NDI | pdb_00006ndi

Crystal Structure of the Sugar Binding Domain of LacI Family Protein from Klebsiella pneumoniae

PDB DOI: https://doi.org/10.2210/pdb6NDI/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Klebsiella pneumoniae subsp. pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-13 Released: 2018-12-26
Deposition Author(s): Minasov, G., Shuvalova, L., Wawrzak, Z., Kiryukhina, O., 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: 2.60 Å
R-Value Free:
0.235 (Depositor), 0.209 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 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: 73.88 kDa
Atom Count: 4,373
Modeled Residue Count: 544
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator	A, B	334	Klebsiella pneumoniae subsp. pneumoniae	Mutation(s): 0 Gene Names: AN676_0312450
UniProt
Find proteins for A0A2W0LW10 (Klebsiella pneumoniae subsp. pneumoniae) Explore A0A2W0LW10 Go to UniProtKB: A0A2W0LW10
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2W0LW10
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.235 (Depositor), 0.209 (DCC)
R-Value Work: 0.182 (Depositor)
R-Value Observed: 0.184 (Depositor)

Diffraction Data:

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.737	α = 90
b = 110.478	β = 97.94
c = 37.777	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-12-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-12-26
Type: Initial release
Version 1.1: 2022-11-30
Changes: Database references, Structure summary
Version 1.2: 2023-06-14
Changes: Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Structure summary