8EP6 | pdb_00008ep6

Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in complex with Avibactam

PDB DOI: https://doi.org/10.2210/pdb8EP6/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Chitinophaga pinensis DSM 2588
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-05 Released: 2022-10-19
Deposition Author(s): Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.187 (Depositor), 0.190 (DCC)
R-Value Work:
0.145 (Depositor), 0.150 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the Beta-lactamase Class D from Chitinophaga pinensis in the complex with Avibactam.

Maltseva, N., Kim, Y., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 29.94 kDa
Atom Count: 2,211
Modeled Residue Count: 245
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase Class D Cpin_0907	A	247	Chitinophaga pinensis DSM 2588	Mutation(s): 0 Gene Names: blaOXA, FEF09_01595
UniProt
Find proteins for A0A5C6M0R4 (Chitinophaga pinensis) Explore A0A5C6M0R4 Go to UniProtKB: A0A5C6M0R4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5C6M0R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C₇ H₁₃ N₃ O₆ S WJDGWXPPFHLLNL-RITPCOANSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.187 (Depositor), 0.190 (DCC)
R-Value Work: 0.145 (Depositor), 0.150 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.816	α = 90
b = 67.864	β = 90
c = 68.698	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-10-19

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Center for Structural Biology of Infectious Diseases (CSBID)

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

Revision History (Full details and data files)

Version 1.0: 2022-10-19
Type: Initial release
Version 1.1: 2023-02-01
Changes: Other, 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.