6HUH | pdb_00006huh

CRYSTAL STRUCTURE OF OXA-427 class D BETA-LACTAMASE

PDB DOI: https://doi.org/10.2210/pdb6HUH/pdb

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

Deposited: 2018-10-08 Released: 2019-10-30
Deposition Author(s): Zavala, A., Retailleau, P., Bogaerts, P., Glupczynski, Y., Naas, T., Iorga, B.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free:
0.269 (Depositor), 0.279 (DCC)
R-Value Work:
0.205 (Depositor), 0.213 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF CMY-OXA-427-HisTag BETA-LACTAMASE

Zavala, A., Naas, T., Bogaerts, P., Glupczynski, Y., Retailleau, P., Iorga, B.I.

To be published.

Macromolecule Content

Total Structure Weight: 61.29 kDa
Atom Count: 3,971
Modeled Residue Count: 484
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	274	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: blaOXA-427, PKLPN57_278 EC: 3.5.2.6
UniProt
Find proteins for A0A1Y6M6D7 (Klebsiella pneumoniae) Explore A0A1Y6M6D7 Go to UniProtKB: A0A1Y6M6D7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Y6M6D7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	C [auth A], D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.269 (Depositor), 0.279 (DCC)
R-Value Work: 0.205 (Depositor), 0.213 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.79	α = 90
b = 42.58	β = 114.37
c = 99.71	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
MrBUMP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-30

Deposition Author(s):

Glupczynski, Y.

Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-LABX-33
French National Research Agency	France	ANR-14-JAMR-0002

Revision History (Full details and data files)

Version 1.0: 2019-10-30
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.