3BFF | pdb_00003bff

class A beta-lactamase SED-G238C complexed with faropenem

PDB DOI: https://doi.org/10.2210/pdb3BFF/pdb

Classification: HYDROLASE
Organism(s): Citrobacter sedlakii
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2007-11-21 Released: 2007-12-18
Deposition Author(s): Pernot, L., Petrella, S., Sougakoff, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.205 (Depositor), 0.200 (DCC)
R-Value Work:
0.180 (Depositor), 0.170 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

acyl-intermediate structures of the class A beta-lactamase SED-G238C

Pernot, L., Petrella, S., Sougakoff, W.

To be published.

Macromolecule Content

Total Structure Weight: 115.17 kDa
Atom Count: 9,194
Modeled Residue Count: 1,048
Deposited Residue Count: 1,048
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class A beta-lactamase Sed1	A, B, C, D	262	Citrobacter sedlakii	Mutation(s): 1 Gene Names: bla-SED-1 EC: 3.5.2.6
UniProt
Find proteins for Q93PQ0 (Citrobacter sedlakii) Explore Q93PQ0 Go to UniProtKB: Q93PQ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q93PQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFR Query on SFR Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], M [auth C], O [auth D]	(2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid C₁₂ H₁₇ N O₆ S CGJDLFMMMJEANA-DAGMQNCNSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
FPM Query on FPM Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	(5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid C₁₂ H₁₅ N O₅ S HGGAKXAHAYOLDJ-FHZUQPTBSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A] G [auth B] H [auth B] I [auth B] K [auth C] E [auth A], G [auth B], H [auth B], I [auth B], K [auth C], N [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.205 (Depositor), 0.200 (DCC)
R-Value Work: 0.180 (Depositor), 0.170 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.116	α = 90
b = 73.244	β = 121.69
c = 103.504	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
MOLREP	phasing
CNS	refinement
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Pernot, L.

Petrella, S.

Sougakoff, W.

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary

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class A beta-lactamase SED-G238C complexed with faropenem

acyl-intermediate structures of the class A beta-lactamase SED-G238C

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations