3LY4 | pdb_00003ly4

Crystal Structure of fluorophore-labeled Class A -lactamase PenP-E166Cb in complex with penicillin G

PDB DOI: https://doi.org/10.2210/pdb3LY4/pdb

Classification: HYDROLASE
Organism(s): Bacillus licheniformis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-02-26 Released: 2011-03-02
Deposition Author(s): Zhao, Y.X., Leung, Y.C., Wong, W.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.260 (Depositor), 0.257 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of fluorophore-labeled Class A -lactamase PenP-E166Cb in complex with penicillin G

Zhao, Y.X., Leung, Y.C., Wong, W.T.

To be published.

Macromolecule Content

Total Structure Weight: 28.93 kDa
Atom Count: 2,173
Modeled Residue Count: 257
Deposited Residue Count: 257
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	257	Bacillus licheniformis	Mutation(s): 1 Gene Names: penP EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808 Go to UniProtKB: P00808
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00808
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PNM Query on PNM 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]	OPEN FORM - PENICILLIN G C₁₆ H₂₀ N₂ O₄ S OGFZUTGOGYUTKZ-KWCYVHTRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.260 (Depositor), 0.257 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.454	α = 90
b = 74.7	β = 90
c = 78.989	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

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Entry History

Deposition Data

Released Date: 2011-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2016-09-28
Changes: Database references, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary

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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.