6XJ3 | pdb_00006xj3

Crystal structure of Class D beta-lactamase from Klebsiella quasipneumoniae in complex with avibactam

PDB DOI: https://doi.org/10.2210/pdb6XJ3/pdb

Classification: HYDROLASE
Organism(s): Klebsiella pneumoniae 700603
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-22 Released: 2020-07-01
Deposition Author(s): Chang, C., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Class D beta-lactamase from Klebsiella quasipneumoniae

Chang, C., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 120.42 kDa
Atom Count: 8,656
Modeled Residue Count: 964
Deposited Residue Count: 1,028
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	257	Klebsiella pneumoniae 700603	Mutation(s): 0 Gene Names: oxa-2, blaOXA-2 EC: 3.5.2.6
UniProt
Find proteins for Q4LAV3 (Klebsiella pneumoniae) Explore Q4LAV3 Go to UniProtKB: Q4LAV3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4LAV3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NXL (Subject of Investigation/LOI) Query on NXL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	E [auth A], H [auth B], N [auth C], P [auth D]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C₇ H₁₃ N₃ O₆ S WJDGWXPPFHLLNL-RITPCOANSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain N [auth C] Focus chain P [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B], K [auth B], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.181 (DCC)
R-Value Observed: 0.182 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.552	α = 90
b = 88.669	β = 99.15
c = 76.1	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary