3BFC

class A beta-lactamase SED-G238C complexed with imipenem

PDB DOI: https://doi.org/10.2210/pdb3BFC/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: 2.20 Å
R-Value Free: 0.242
R-Value Work: 0.206
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 114.53 kDa
Atom Count: 8,648
Modelled 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IM2 Query on IM2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C₁₂ H₁₉ N₃ O₄ S UACUABDJLSUFFC-IWSPIJDZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.242
R-Value Work: 0.206
R-Value Observed: 0.215
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.436	α = 90
b = 73.399	β = 122.36
c = 105.05	γ = 90

Software Package:

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

Structure Validation

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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: 2011-08-24
Changes: Non-polymer description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Deposit Data

Help and Resources

3BFC

class A beta-lactamase SED-G238C complexed with imipenem

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)