3C5A | pdb_00003c5a

Crystal structure of the C-terminal deleted mutant of the class A carbapenemase KPC-2 at 1.23 angstrom

PDB DOI: https://doi.org/10.2210/pdb3C5A/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-31 Released: 2008-08-05
Deposition Author(s): Petrella, S., Ziental-Gelus, N., Mayer, C., Jarlier, V., Sougakoff, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free:
0.196 (Depositor), 0.183 (DCC)
R-Value Work:
0.181 (Depositor), 0.165 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3C5A

This is version 1.3 of the entry. See complete history.

Literature

Genetic and structural insights into the dissemination potential of the extremely-broad-spectrum class A {beta}-lactamase (EBSBL) KPC-2 identified in two strains of Escherichia coli and Enterobacter cloacae isolated from the same patient in France

Petrella, S., Ziental-Gelus, N., Mayer, C., Renard, M., Jarlier, V., Sougakoff, W.

(2008) Antimicrob Agents Chemother

Macromolecule Content

Total Structure Weight: 28.18 kDa
Atom Count: 2,168
Modeled Residue Count: 264
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class A carbapenemase KPC-2	A	264	Escherichia coli	Mutation(s): 0 EC: 3.5.2.6
UniProt
Find proteins for A8DS27 (Escherichia coli) Explore A8DS27 Go to UniProtKB: A8DS27
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8DS27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT 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]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.23 Å
R-Value Free: 0.196 (Depositor), 0.183 (DCC)
R-Value Work: 0.181 (Depositor), 0.165 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.89	α = 90
b = 65.99	β = 90
c = 72.13	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Xnemo	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Ziental-Gelus, N.

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.